Methods of improving drought tolerance and seed production in rice

ABSTRACT

The invention provides for compositions and methods for producing plants that have higher yield in drought conditions by manipulating the G-proteins such as the rice alpha subunit gene, RGA1. In particular, the present invention provides for plants, varieties, lines, and hybrids, as well as plant tissues and plant seeds that contain modified G-protein activity, particularly RGA1 activity to engineer drought tolerance and improved seed production in plants, as well as improved tolerance to high density planting

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Divisional application of U.S. Ser. No. 13/866,401filed Apr. 19, 2013, which claims priority under 35 U.S.C. §119 toprovisional application Ser. No. 61/665,385 filed Jun. 28, 2012, hereinincorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

Rice is one of the three major cereal crops and is a staple food formore than a third of the world's population. Drought is one of the majorabiotic stress factors limiting crop productivity worldwide. Globalclimate changes may further exacerbate the drought situation in majorcrop-producing countries. Although irrigation may in theory solve thedrought problem, it is usually not a viable option because of the costassociated with building and maintaining an effective irrigation system,as well as other issues, such as the general availability of water.Thus, alternative means for alleviating plant water stress are needed.

Upon exposure of plants to drought conditions, many stress-related genesare induced and their products are thought to function as cellularprotectants of stress-induced damage. The expression of stress-relatedgenes is largely regulated by specific transcription factors. Members ofthe AP2, bZIP, zinc finger, and MYB families have been shown to haveregulatory roles in stress responses. The rice and Arabidopsis genomescode for more than 1300 transcriptional regulators, accounting for about6% of the estimated total number of genes in both cases. About 45% ofthese transcription factors were reported to be from plant-specificfamilies (Riechmann et al., (2000) Science 290: 2105-2110).

Plant modification for enhanced drought tolerance is mostly based on themanipulation of either transcription and/or signaling factors or genesthat directly protect plant cells against water deficit. Despite muchprogress in the field, understanding the basic biochemical and molecularmechanisms for drought stress perception, transduction, response andtolerance remains a major challenge. Utilization of the knowledge ondrought tolerance to generate plants that can endure under extreme waterdeficit condition is even a bigger challenge.

Rice is a staple food for greater than one third of the world'spopulation and worldwide total rice planting area is approximately 1.5million square kilometers. In 2009 global rice production was over 670million tons, second only to maize.

Approximately 20% of rice growing areas worldwide are prone to drought.Drought is a particularly important issue for rice production. About5000 liters of water are needed to produce one kilogram of rice,approximately double the needs of other crops.

Despite efforts to develop drought-tolerant rice plants, very fewattempts have been shown to improve grain yields. Examples of positiveeffects include transgenic rice plants expressing SNAC1 (Hu et al.,(2006) Proc Natl Acad Sci USA 103: 12987-12992) and OsLEA3 (Xiao at al.,(2007) Theor Appl Genet 115: 35-46), which was shown to improve grainyield under field drought conditions.

Heterotrimeric G-proteins are key signal transduction components thatcouple the perception of an external signal by a G-protein coupledreceptor (GPCR) to downstream effectors. More than one third ofmammalian signaling pathways depend on heterotrimeric G-proteins,including vision, taste, olfaction, hormones, and neurotransmitters.G-protein coupled signaling pathways are targets of approximately halfof all pharmaceuticals.

The G-protein complex is comprised of Gα, Gβ and Gγ monomeric subunitsthat assemble as a heterotrimer that physically associates with a GPCR.Activation of the GPCR triggers the Gα subunit to exchange GDP for GTP,thus activating the G-protein. Once active the heterotrimeric complexdissociates from the GPCR and the Gα subunit separates from the Gβγheterodimer. Both GTP-bound Gα and the Gβγ heterodimer transduce thesignal to downstream effectors.

Heterotrimeric G-proteins have been studied extensively in animals. Todate, 23 Gα, 6 Gβ and 11 Gγ genes have been reported in mammals(Vanderbeld and Kelly (2000) Biochem. Cell Biol. 78: 537-550). The alphasubunits are classified into four subfamilies: Gs, Gi, Gq, and G₁₂. Incontrast, relatively little is known about the role G-proteins play inplants. Loss-of-function mutants in the Gα subunit of rice andArabidopsis are completely viable, but show several characteristicdevelopmental attributes. The rice mutant exhibits shortened internodes,rounded seeds, and partial insensitivity to gibberellin, whereas theArabidopsis mutants have rounded leaves and altered sensitivity to anumber of phytohormones (Ashikari et al. (1999) Proc. Natl. Acad. Sci.96: 10284-10289; Fujisawa et al. (1999) Proc. Natl. Acad. Sci.96:7575-7580; Ueguchi-Tanaka et al. (2000) Proc. Natl. Acad. Sci. 97:11638-11643; Wang et al. (2001) Science 292: 2070-2072; (Ullah et al.(2001) Science 292: 2066-2069). A loss-of-function mutant in the Gβsubunit of Arabidopsis (AGB1) exhibits several defects including short,blunt fruits, rounded leaves, and shortened floral buds (Lease et al.(2001) Plant Cell 13: 2631-2641).

It can be seen that there is a continuing need to develop droughttolerance in plants, particularly rice.

It is an object of the present invention to modulate Gα proteins such asRGA1, in plants to engineer drought tolerance and increase seed yieldunder such conditions.

Other objects will become apparent from the description of theinvention, which follows.

SUMMARY OF THE INVENTION

The rice dwarf mutant, d1, contains a non-functional RGA1 gene, encodingthe GTP-binding α-subunit of the heterotrimeric G protein. Rice RGA1encodes a 380 amino acid Gα protein. Applicants have identified a 2 bpdeletion (allele d1), which results in a frameshift mutation resultingin a predicted protein truncation after amino acid 304. This mutant wasoriginally isolated as a spontaneous mutant with reduced height andshorter, erect, thicker, broad, dark green leaves, compact panicles, andshort, round grains. Applicants have identified that a non-functionalRGA1 gene or other related G-proteins can be used to create higher seedproduction and yield under drought conditions. The d1 plants alsoperform better at higher planting density.

Thus the present invention provides for compositions and methods forproducing plants that have higher yield in drought conditions bymanipulating the G-proteins such as the RGA1 gene. In particular, thepresent invention provides for plants, varieties, lines, and hybrids, aswell as plant tissues and plant seeds that contain modified G-proteinactivity, particularly RGA1 activity to engineer drought tolerance andimproved seed production in plants.

In one embodiment, the present invention provides for one or more plantswhose germplasm has been modified to render a G-protein, particularlythe RGA1 gene or its gene product inactive. Moreover, in furtherembodiments the invention relates to the offspring (e.g., F1, F2, F3,etc.) of a cross of said plant wherein the germplasm of said offspringhas the same mutation as the parent plant. Therefore, embodiments of thepresent invention provide for plant varieties/hybrids whose germplasmcontains a mutation, such that the phenotype of the plants isnon-functional RGA1 gene activity in drought conditions. In someembodiments, said offspring (e.g., F1, F2, F3, etc.) are the result of across between elite lines, at least one of which contains a germplasmcomprising a mutation that renders the G-protein such as RGA1 protein orgene of said plant inactive, particularly during drought.

In another embodiment, the present invention provides a method ofimproving seed development in drought conditions comprising inhibitingthe activity of a G-protein, such as an RGA1 protein during droughtconditions.

In another embodiment, the present invention provides a hybrid plant,line or variety, wherein said plant hybrid, line or variety comprisesgermplasm comprising one or more mutations in a G-protein encoding gene,or the RGA1 gene such that the G-protein or RGA1 protein is inactiveduring drought conditions. This can be by use of a naturally occurringmutation such as the d1 mutant, or preferably by introduction anexpression cassette to said plant designed to reduce activity of theRGA1 or other related G-protein gene either constitutively or underdrought conditions.

In some embodiments, said plant hybrid, line or variety is created byintrogression of a plant germplasm that comprises said one or moremodifications for rendering a G-protein or RGA1 gene or its encodedprotein product inactive. In some embodiments, said plant hybrid, lineor variety is created by incorporation of a heterologous geneticconstruct comprising designed to inhibit or otherwise decrease G-proteinactivity, particularly during drought conditions.

In another embodiment, the present invention provides a method forproducing a plant hybrid, line or variety resistant to droughtconditions and with improved seed production compared to a wild typeplant under the same conditions comprising identifying a germplasm witha null G-protein or RGA1 modification, and introducing said germplasminto an elite plant hybrid, line or variety. In some embodiments, saidintroducing of said germplasm into said elite hybrid, line or variety isby introgression. In some embodiments, said introducing of saidgermplasm into said elite plant hybrid, line or variety is byintroduction of a heterologous genetic construct.

In yet another embodiment, the present invention provides a planthybrid, line or variety wherein the germplasm of said hybrid, line orvariety confers drought tolerance with improved seed production.

In yet another embodiment, the present invention provides a method foridentifying plant lines resistant to drought comprising supplying anucleic acid sample from a plant, providing amplification primers foramplifying a region of a plant corresponding to an G-protein or RGA1nucleic acid sample, applying said amplification primers to said nucleicacid sample such that amplification of said region of said G-proteingene occurs, and identifying plants resistant to drought based on thepresence of one or more null mutations in said amplified nucleic acidsample.

In still another embodiment, the present invention provides for seedswherein said germplasm of said seeds comprises a modified G-protein orRGA1 gene such that said mutation confers improved seed production underdrought conditions.

In some embodiments, the present invention provides for a plant thatcomprises a heterologous nucleotide sequence that is at least 70%homologous, at least 80% homologous, at least 85% homologous, at least90% homologous, at least 95% homologous, at least 97% homologous, or atleast 99% homologous to the RGA1 gene of SEQ ID NO: 1, 2, 5, or 6. Theinvention also includes RGA1 polypeptides including the amino acidsequences of SEQ ID NO:3 or 4, conservatively modified variants whichretain activity or loss of activity thereof as applicable.

In one embodiment, the present invention provides a method of producingplant seed comprising crossing a plant comprising a genetically modifiedG-protein or a genetically modified RGA1 gene with itself or a secondplant and collecting said seed from said cross. In some embodiments, themethods for producing said seed comprises planting a parent seed linewherein said parent seed line comprises a germplasm confers a decreasein activity or a G-protein or RGA1 mutation with a parent pollinatorplant line wherein said pollinator and/or seed line germplasm comprisesa germplasm that confers a modified G-protein or RGA1 protein, growingsaid parent seed and pollinator plants together, allowing for the saidparent seed plants to be pollinated by said parent pollinator plants,and harvesting the seed that results from said pollination.

In yet another embodiment, the invention provides for geneticallymodified plants incorporating a heterologous nucleotide constructencoding a RGA1 gene such as SEQ ID NOS: 1, 2, 5, or 6 operably linkedto regulatory sequences such as expression cassettes, inhibitionconstructs, plants, plant cells, and seeds. The genetically modifiedplants, plant cells, and seeds of the invention may exhibit phenotypicchanges, such as modulated RGA1 activity, particularly during droughtconditions.

Methods are provided for reducing or eliminating the activity of aG-protein or RGA1 polypeptide in a plant, comprising introducing intothe plant a selected polynucleotide. In specific methods, providing thepolynucleotide decreases the level of RGA1 or related G-protein in theplant.

Methods are also provided for increasing the level of a modified RGA1 orG-protein polypeptide in a plant either constitutively or atspecifically regulated times and tissues comprising introducing into theplant a selected polynucleotide with appropriate regulatory elements. Inspecific methods, expression of the modified RGA1 or G-proteinpolynucleotide improves the plants' tolerance to drought.

DEFINITIONS

Units, prefixes, and symbols may be denoted in their SI accepted form.Unless otherwise indicated, nucleic acids are written left to right in5′ to 3′ orientation; amino acid sequences are written left to right inamino to carboxy orientation, respectively. Numeric ranges are inclusiveof the numbers defining the range and include each integer within thedefined range. Amino acids may be referred to herein by either theircommonly known three letter symbols or by the one-letter symbolsrecommended by the IUPAC-IUB Biochemical nomenclature Commission.Nucleotides, likewise, may be referred to by their commonly acceptedsingle-letter codes. Unless otherwise provided for, software,electrical, and electronics terms as used herein are as defined in TheNew IEEE Standard Dictionary of Electrical and Electronics Terms (5thEdition, 1993). The terms defined below are more fully defined byreference to the specification as a whole.

By “amplified” is meant the construction of multiple copies of a nucleicacid sequence or multiple copies complementary to the nucleic acidsequence using at least one of the nucleic acid sequences as a template.Amplification systems include the polymerase chain reaction (PCR)system, ligase chain reaction (LCR) system, nucleic acid sequence basedamplification (NASBA, Canteen, Mississauga, Ontario), Q-Beta Replicasesystems, transcription-based amplification system (TAS), and stranddisplacement amplification (SDA). See, e.g., Diagnostic MolecularMicrobiology: Principles and Applications, D. H. Persing et al., Ed.,American Society for Microbiology, Washington, D.C. (1993). The productof amplification is termed an amplicon.

As used herein, “chromosomal region” includes reference to a length of achromosome that may be measured by reference to the linear segment ofDNA that it comprises. The chromosomal region can be defined byreference to two unique DNA sequences, i.e., markers.

The term “conservatively modified variants” applies to both amino acidand nucleic acid sequences. With respect to particular nucleic acidsequences, “conservatively modified variants” refers to those nucleicacids which encode identical or conservatively modified variants of theamino acid sequences. Because of the degeneracy of the genetic code, alarge number of functionally identical nucleic acids encode any givenprotein. For instance, the codons GCA, GCC, GCG and GCU all encode theamino acid alanine. Thus, at every position where an alanine isspecified by a codon, the codon can be altered to any of thecorresponding codons described without altering the encoded polypeptide.Such nucleic acid variations are “silent variations” and represent onespecies of conservatively modified variation. Every nucleic acidsequence herein that encodes a polypeptide also, by reference to thegenetic code, describes every possible silent variation of the nucleicacid. One of ordinary skill will recognize that each codon in a nucleicacid (except AUG, which is ordinarily the only codon for methionine; andUGG, which is ordinarily the only codon for tryptophan) can be modifiedto yield a functionally identical molecule. Accordingly, each silentvariation of a nucleic acid, which encodes a polypeptide of the presentinvention, is implicit in each described polypeptide sequence and iswithin the scope of the present invention.

As to amino acid sequences, one of skill will recognize that individualsubstitutions, deletions or additions to a nucleic acid, peptide,polypeptide, or protein sequence which alters, adds or deletes a singleamino acid or a small percentage of amino acids in the encoded sequenceis a “conservatively modified variant” where the alteration results inthe substitution of an amino acid with a chemically similar amino acid.Thus, any number of amino acid residues selected from the group ofintegers consisting of from 1 to 15 can be so altered. Thus, forexample, 1, 2, 3, 4, 5, 7, or 10 alterations can be made. Conservativelymodified variants typically provide similar biological activity as theunmodified polypeptide sequence from which they are derived. Forexample, substrate specificity, enzyme activity, or ligand/receptorbinding is generally at least 30%, 40%, 50%, 60%, 70%, 80%, or 90% ofthe native protein for its native substrate. Conservative substitutiontables providing functionally similar amino acids are well known in theart.

The following six groups each contain amino acids that are conservativesubstitutions for one another:

1) Alanine (A), Serine (S), Threonine (T);

2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and

6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

See also, Creighton (1984) Proteins W.H. Freeman and Company.

By “encoding” or “encoded”, with respect to a specified nucleic acid, ismeant comprising the information for translation into the specifiedprotein. A nucleic acid encoding a protein may comprise non-translatedsequences (e.g., introns) within translated regions of the nucleic acid,or may lack such intervening non-translated sequences (e.g., as incDNA). The information by which a protein is encoded is specified by theuse of codons. Typically, the amino acid sequence is encoded by thenucleic acid using the “universal” genetic code. However, variants ofthe universal code, such as are present in some plant, animal, andfungal mitochondria, the bacterium Mycoplasma capricolum, or the ciliateMacronucleus, may be used when the nucleic acid is expressed therein.

When the nucleic acid is prepared or altered synthetically, advantagecan be taken of known codon preferences of the intended host where thenucleic acid is to be expressed. For example, although nucleic acidsequences of the present invention may be expressed in bothmonocotyledonous and dicotyledonous plant species, sequences can bemodified to account for the specific codon preferences and GC contentpreferences of monocotyledons or dicotyledons as these preferences havebeen shown to differ (Murray et al. Nucl. Acids Res. 17:477-498 (1989)).

As used herein “full-length sequence” in reference to a specifiedpolynucleotide or its encoded protein means having the entire amino acidsequence of, a native (non-synthetic), endogenous, biologically activeform of the specified protein. Methods to determine whether a sequenceis full-length are well known in the art including such exemplarytechniques as northern or western blots, primer extensions, S1protection, and ribonuclease protection. See, e.g., Plant MolecularBiology: A Laboratory Manual, Clark, Ed., Springer-Verlag, Berlin(1997). Comparison to known full-length homologous (orthologous and/orparalogous) sequences can also be used to identify full-length sequencesof the present invention. Additionally, consensus sequences typicallypresent at the 5′ and 3′ untranslated regions of mRNA aid in theidentification of a polynucleotide as full-length. For example, theconsensus sequence ANNNNAUGG, where the underlined codon represents theN-terminal methionine, aids in determining whether the polynucleotidehas a complete 5′ end. Consensus sequences at the 3′ end, such aspolyadenylation sequences, aid in determining whether the polynucleotidehas a complete 3′ end.

As used herein, “heterologous” in reference to a nucleic acid is anucleic acid that originates from a foreign species, or, if from thesame species, is substantially modified from its native form incomposition and/or genomic locus by deliberate human intervention. Forexample, a promoter operably linked to a heterologous structural gene isfrom a species different from that from which the structural gene wasderived, or, if from the same species, one or both are substantiallymodified from their original form. A heterologous protein may originatefrom a foreign species or, if from the same species, is substantiallymodified from its original form by deliberate human intervention.

By “host cell” is meant a cell which contains a vector and supports thereplication and/or expression of the vector. Host cells may beprokaryotic cells such as E. coli, or eukaryotic cells such as yeast,insect, amphibian, or mammalian cells. Preferably, host cells aremonocotyledonous or dicotyledonous plant cells. A particularly preferredmonocotyledonous host cell is a maize host cell.

The term “hybridization complex” includes reference to a duplex nucleicacid structure formed by two single-stranded nucleic acid sequencesselectively hybridized with each other.

The term “introduced” in the context of inserting a nucleic acid into acell, means “transfection” or “transformation” or “transduction” andincludes reference to the incorporation of a nucleic acid into aeukaryotic or prokaryotic cell where the nucleic acid may beincorporated into the genome of the cell (e.g., chromosome, plasmid,plastid or mitochondrial DNA), converted into an autonomous replicon, ortransiently expressed (e.g., transfected mRNA).

The term “isolated” refers to material, such as a nucleic acid or aprotein, which is: (1) substantially or essentially free from componentsthat normally accompany or interact with it as found in its naturallyoccurring environment. The isolated material optionally comprisesmaterial not found with the material in its natural environment; or (2)if the material is in its natural environment, the material has beensynthetically (non-naturally) altered by deliberate human interventionto a composition and/or placed at a location in the cell (e.g., genomeor subcellular organelle) not native to a material found in thatenvironment. The alteration to yield the synthetic material can beperformed on the material within or removed from its natural state. Forexample, a naturally occurring nucleic acid becomes an isolated nucleicacid if it is altered, or if it is transcribed from DNA which has beenaltered, by means of human intervention performed within the cell fromwhich it originates. See, e.g., Compounds and Methods for Site DirectedMutagenesis in Eukaryotic Cells, Kmiec, U.S. Pat. No. 5,565,350; In VivoHomologous Sequence Targeting in Eukaryotic Cells; Zarling et al.,PCT/US93/03868. Likewise, a naturally occurring nucleic acid (e.g., apromoter) becomes isolated if it is introduced by non-naturallyoccurring means to a locus of the genome not native to that nucleicacid. Nucleic acids which are “isolated” as defined herein are alsoreferred to as “heterologous” nucleic acids.

As used herein, “localized within the chromosomal region defined by andincluding” with respect to particular markers includes reference to acontiguous length of a chromosome delimited by and including the statedmarkers.

As used herein, “marker” includes reference to a locus on a chromosomethat serves to identify a unique position on the chromosome. A“polymorphic marker” includes reference to a marker which appears inmultiple forms (alleles) such that different forms of the marker, whenthey are present in a homologous pair, allow transmission of each of thechromosomes of that pair to be followed. A genotype may be defined byuse of one or a plurality of markers.

By “nucleic acid library” is meant a collection of isolated DNA or cDNAmolecules which comprise and substantially represent the entiretranscribed fraction of a genome of a specified organism. Constructionof exemplary nucleic acid libraries, such as genomic and cDNA libraries,is taught in standard molecular biology references such as Berger andKimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology,Vol. 152, Academic Press, Inc., San Diego, Calif. (Berger); Sambrook etal., Molecular Cloning—A Laboratory Manual, 2nd ed., Vol. 1-3 (1989);and Current Protocols in Molecular Biology, F. M. Ausubel et al., Eds.,Current Protocols, a joint venture between Greene Publishing Associates,Inc. and John Wiley & Sons, Inc. (1994).

As used herein, “operably linked” includes reference to a functionallinkage between a promoter and a second sequence, wherein the promotersequence initiates and mediates transcription of the DNA sequencecorresponding to the second sequence. Generally, “operably linked” meansthat the nucleic acid sequences being linked are contiguous and, wherenecessary to join two protein coding regions, contiguous and in the samereading frame.

As used herein, the term “plant” can include reference to whole plants,plant parts or organs (e.g., leaves, stems, roots, etc.), plant cells,seeds and progeny of same. Plant cell, as used herein, further includes,without limitation, cells obtained from or found in: seeds, suspensioncultures, embryos, meristematic regions, callus tissue, leaves, roots,shoots, gametophytes, sporophytes, pollen, and microspores. Plant cellscan also be understood to include modified cells, such as protoplasts,obtained from the aforementioned tissues. The class of plants which canbe used in the methods of the invention is generally as broad as theclass of higher plants amenable to transformation techniques, includingboth monocotyledonous and dicotyledonous plants. Particularly preferredplants include maize, soybean, sunflower, sorghum, canola, wheat,alfalfa, cotton, rice, barley, and millet.

As used herein, “polynucleotide” includes reference to adeoxyribopolynucleotide, ribopolynucleotide, or analogs thereof thathave the essential nature of a natural ribonucleotide in that theyhybridize, under stringent hybridization conditions, to substantiallythe same nucleotide sequence as naturally occurring nucleotides and/orallow translation into the same amino acid(s) as the naturally occurringnucleotide(s). A polynucleotide can be full-length or a subsequence of anative or heterologous structural or regulatory gene. Unless otherwiseindicated, the term includes reference to the specified sequence as wellas the complementary sequence thereof. Thus, DNAs or RNAs with backbonesmodified for stability or for other reasons as “polynucleotides” as thatterm is intended herein. Moreover, DNAs or RNAs comprising unusualbases, such as inosine, or modified bases, such as tritylated bases, toname just two examples, are polynucleotides as the term is used herein.It will be appreciated that a great variety of modifications have beenmade to DNA and RNA that serve many useful purposes known to those ofskill in the art. The term polynucleotide as it is employed hereinembraces such chemically, enzymatically or metabolically modified formsof polynucleotides, as well as the chemical forms of DNA and RNAcharacteristic of viruses and cells, including among other things,simple and complex cells.

The terms “polypeptide”, “peptide” and “protein” are usedinterchangeably herein to refer to a polymer of amino acid residues. Theterms apply to amino acid polymers in which one or more amino acidresidues is an artificial chemical analogue of a corresponding naturallyoccurring amino acid, as well as to naturally occurring amino acidpolymers. The essential nature of such analogues of naturally occurringamino acids is that, when incorporated into a protein, that protein isspecifically reactive to antibodies elicited to the same protein butconsisting entirely of naturally occurring amino acids. The terms“polypeptide”, “peptide” and “protein” are also inclusive ofmodifications including, but not limited to, glycosylation, lipidattachment, sulfation, gamma-carboxylation of glutamic acid residues,hydroxylation and ADP-ribosylation. It will be appreciated, as is wellknown and as noted above, that polypeptides are not entirely linear. Forinstance, polypeptides may be branched as a result of ubiquitination,and they may be circular, with or without branching, generally as aresult of posttranslation events, including natural processing event andevents brought about by human manipulation which do not occur naturally.Circular, branched and branched circular polypeptides may be synthesizedby non-translation natural process and by entirely synthetic methods, aswell. Further, this invention contemplates the use of both themethionine-containing and the methionine-less amino terminal variants ofthe protein of the invention.

As used herein “promoter” includes reference to a region of DNA upstreamfrom the start of transcription and involved in recognition and bindingof RNA polymerase and other proteins to initiate transcription. A “plantpromoter” is a promoter capable of initiating transcription in plantcells whether or not its origin is a plant cell. Exemplary plantpromoters include, but are not limited to, those that are obtained fromplants, plant viruses, and bacteria which comprise genes expressed inplant cells such as Agrobacterium or Rhizobium. Examples of promotersunder developmental control include promoters that preferentiallyinitiate transcription in certain tissues, such as leaves, roots, orseeds. Such promoters are referred to as “tissue preferred”. Promoterswhich initiate transcription only in certain tissue are referred to as“tissue specific”. A “cell type” specific promoter primarily drivesexpression in certain cell types in one or more organs, for example,vascular cells in roots or leaves. An “inducible” or “repressible”promoter is a promoter which is under environmental control. Examples ofenvironmental conditions that may affect transcription by induciblepromoters include anaerobic conditions or the presence of light. Tissuespecific, tissue preferred, cell type specific, and inducible promotersconstitute the class of “non-constitutive” promoters. A “constitutive”promoter is a promoter which is active under most environmentalconditions.

As used herein “recombinant” includes reference to a cell or vector thathas been modified by the introduction of a heterologous nucleic acid orthat the cell is derived from a cell so modified. Thus, for example,recombinant cells express genes that are not found in identical formwithin the native (non-recombinant) form of the cell or express nativegenes that are otherwise abnormally expressed, under-expressed or notexpressed at all as a result of deliberate human intervention. The term“recombinant” as used herein does not encompass the alteration of thecell or vector by naturally occurring events (e.g., spontaneousmutation, natural transformation/transduction/transposition) such asthose occurring without deliberate human intervention.

As used herein, a “recombinant expression cassette” is a nucleic acidconstruct, generated recombinantly or synthetically, with a series ofspecified nucleic acid elements which permit transcription of aparticular nucleic acid in a host cell. The recombinant expressioncassette can be incorporated into a plasmid, chromosome, mitochondrialDNA, plastid DNA, virus, or nucleic acid fragment. Typically, therecombinant expression cassette portion of an expression vectorincludes, among other sequences, nucleic acids to be transcribed, and apromoter.

The terms “residue” or “amino acid residue” or “amino acid” are usedinterchangeably herein to refer to an amino acid that is incorporatedinto a protein, polypeptide, or peptide (collectively “protein”). Theamino acid may be a naturally occurring amino acid and, unless otherwiselimited, may encompass non-natural analogs of natural amino acids thatcan function in a similar manner as naturally occurring amino acids.

The term “selectively hybridizes” includes reference to hybridization,under stringent hybridization conditions, of a nucleic acid sequence toa specified nucleic acid target sequence to a detectably greater degree(e.g., at least 2-fold over background) than its hybridization tonon-target nucleic acid sequences and to the substantial exclusion ofnon-target nucleic acids. Selectively hybridizing sequences typicallyhave about at least 80% sequence identity, preferably 90% sequenceidentity, and most preferably 100% sequence identity (i.e.,complementary) with each other.

The term “stringent conditions” or “stringent hybridization conditions”includes reference to conditions under which a probe will hybridize toits target sequence, to a detectably greater degree than to othersequences (e.g., at least 2-fold over background). Stringent conditionsare sequence-dependent and can be different in different circumstances.By controlling the stringency of the hybridization and/or washingconditions, target sequences can be identified which are 100%complementary to the probe (homologous probing). Alternatively,stringency conditions can be adjusted to allow some mismatching insequences so that lower degrees of similarity are detected (heterologousprobing). Generally, a probe is less than about 1000 nucleotides inlength, optionally less than 500 nucleotides in length.

Typically, stringent conditions will be those in which the saltconcentration is less than about 1.5 M Na⁺ ion, typically about 0.01 to1.0 M Na⁺ ion concentration (or other salts) at pH 7.0 to 8.3 and thetemperature is at least about 30° C. for short probes (e.g., 10 to 50nucleotides) and at least about 60° C. for long probes (e.g., greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide. Exemplary lowstringency conditions include hybridization with a buffer solution of 30to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C.,and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at50 to 55° C. Exemplary moderate stringency conditions includehybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37° C., and awash in 0.5× to 1×SSC at 55 to 50° C. Exemplary high stringencyconditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at37° C., and a wash in 0.1×SSC at 60 to 65° C. for 20 minutes.

Specificity is typically the function of post-hybridization washes, thecritical factors being the ionic strength and temperature of the finalwash solution. For DNA-DNA hybrids, the T_(m) can be approximated fromthe equation of Meinkoth and Wahl, Anal. Biochem., 138:267-284 (1984):T_(m)=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M isthe molarity of monovalent cations, % GC is the percentage of guanosineand cytosine nucleotides in the DNA, % form is the percentage offormamide in the hybridization solution, and L is the length of thehybrid in base pairs. The T_(m) is the temperature (under defined ionicstrength and pH) at which 50% of the complementary target sequencehybridizes to a perfectly matched probe. T_(m) is reduced by about 1° C.for each 1% of mismatching; thus, T_(m), hybridization and/or washconditions can be adjusted to hybridize to sequences of the desiredidentity. For example, if sequences with 90% identity are sought, theT_(m) can be decreased 10° C. Generally, stringent conditions areselected to be about 5° C. lower than the thermal melting point (T_(m))for the specific sequence and its complement at a defined ionic strengthand pH. However, severely stringent conditions can utilize ahybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermalmelting point (T_(m)); moderately stringent conditions can utilize ahybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than thethermal melting point (T_(m)); low stringency conditions can utilize ahybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower thanthe thermal melting point (T_(m)). Using the equation, hybridization andwash compositions, and desired T_(m), those of ordinary skill willunderstand that variations in the stringency of hybridization and/orwash solutions are inherently described. If the desired degree ofmismatching results in a T_(m) of less than 45° C. (aqueous solution) or32° C. (formamide solution) it is preferred to increase the SSCconcentration so that a higher temperature can be used. An extensiveguide to the hybridization of nucleic acids is found in Tijssen,Laboratory Techniques in Biochemistry and MolecularBiology—Hybridization with Nucleic Acids Probes, Part I, Chapter 2,Ausubel, et al., Eds., Greene Publishing and Wiley-Interscience, NewYork (1995). In general a high stringency wash is 2×15 min in 0.5×SSCcontaining 0.1% SDS at 65° C.

As used herein, “genetically modified plant” includes reference to aplant which comprises within its genome a heterologous polynucleotide.Generally, the heterologous polynucleotide is stably integrated withinthe genome such that the polynucleotide is passed on to successivegenerations. The heterologous polynucleotide may be integrated into thegenome alone or as part of a recombinant expression cassette.“Transgenic” is used herein to include any cell, cell line, callus,tissue, plant part or plant, the genotype of which has been altered bythe presence of heterologous nucleic acid including those transgenicsinitially so altered as well as those created by sexual crosses orasexual propagation from the initial transgenic. The term “transgenic”or “genetically modified” as used herein does not encompass thealteration of the genome (chromosomal or extra-chromosomal) byconventional plant breeding methods or by naturally occurring eventssuch as random cross-fertilization, non-recombinant viral infection,non-recombinant bacterial transformation, non-recombinant transposition,or spontaneous mutation.

As used herein, “vector” includes reference to a nucleic acid used intransfection of a host cell and into which can be inserted apolynucleotide. Vectors are often replicons. Expression vectors permittranscription of a nucleic acid inserted therein.

The following terms are used to describe the sequence relationshipsbetween two or more nucleic acids or polynucleotides: (a) “referencesequence”, (b) “comparison window”, (c) “sequence identity”, (d)“percentage of sequence identity”, and (e) “substantial identity”.

(a) As used herein, “reference sequence” is a defined sequence used as abasis for sequence comparison. A reference sequence may be a subset orthe entirety of a specified sequence; for example, as a segment of afull-length cDNA or gene sequence, or the complete cDNA or genesequence.

(b) As used herein, “comparison window” includes reference to acontiguous and specified segment of a polynucleotide sequence, whereinthe polynucleotide sequence may be compared to a reference sequence andwherein the portion of the polynucleotide sequence in the comparisonwindow may comprise additions or deletions (i.e., gaps) compared to thereference sequence (which does not comprise additions or deletions) foroptimal alignment of the two sequences. Generally, the comparison windowis at least 20 contiguous nucleotides in length, and optionally can be30, 40, 50, 100, or longer. Those of skill in the art understand that toavoid a high similarity to a reference sequence due to inclusion of gapsin the polynucleotide sequence, a gap penalty is typically introducedand is subtracted from the number of matches.

Methods of alignment of sequences for comparison are well-known in theart. Optimal alignment of sequences for comparison may be conducted bythe local homology algorithm of Smith and Waterman, Adv. Appl. Math.2:482 (1981); by the homology alignment algorithm of Needleman andWunsch, J. Mol. Biol. 48:443 (1970); by the search for similarity methodof Pearson and Lipman, Proc. Natl. Acad. Sci. 85:2444 (1988); bycomputerized implementations of these algorithms, including, but notlimited to: CLUSTAL in the PC/Gene program by Intelligenetics, MountainView, Calif.; GAP, BESTFIT, BLAST, FASTA, and TFASTA in the WisconsinGenetics Software Package, Genetics Computer Group (GCG), 575 ScienceDr., Madison, Wis., USA; the CLUSTAL program is well described byHiggins and Sharp, Gene 73:237-244 (1988); Higgins and Sharp, CABIOS5:151-153 (1989); Corpet, et al., Nucleic Acids Research 16:10881-90(1988); Huang, et al., Computer Applications in the Biosciences 8:155-65(1992), and Pearson, et al., Methods in Molecular Biology 24:307-331(1994). The BLAST family of programs which can be used for databasesimilarity searches includes: BLASTN for nucleotide query sequencesagainst nucleotide database sequences; BLASTX for nucleotide querysequences against protein database sequences; BLASTP for protein querysequences against protein database sequences; TBLASTN for protein querysequences against nucleotide database sequences; and TBLASTX fornucleotide query sequences against nucleotide database sequences. See,Current Protocols in Molecular Biology, Chapter 19, Ausubel, et al.,Eds., Greene Publishing and Wiley-Interscience, New York (1995).

Unless otherwise stated, sequence identity/similarity values providedherein refer to the value obtained using the BLAST 2.0 suite of programsusing default parameters. Altschul et al., Nucleic Acids Res.25:3389-3402 (1997). Software for performing BLAST analyses is publiclyavailable, e.g., through the National Center forBiotechnology-Information World Wide Web at ncbi.nih.gov. This algorithminvolves first identifying high scoring sequence pairs (HSPs) byidentifying short words of length W in the query sequence, which eithermatch or satisfy some positive-valued threshold score T when alignedwith a word of the same length in a database sequence. T is referred toas the neighborhood word score threshold (Altschul et al., supra). Theseinitial neighborhood word hits act as seeds for initiating searches tofind longer HSPs containing them. The word hits are then extended inboth directions along each sequence for as far as the cumulativealignment score can be increased. Cumulative scores are calculatedusing, for nucleotide sequences, the parameters M (reward score for apair of matching residues; always >0) and N (penalty score formismatching residues; always <0). For amino acid sequences, a scoringmatrix is used to calculate the cumulative score. Extension of the wordhits in each direction are halted when: the cumulative alignment scorefalls off by the quantity X from its maximum achieved value; thecumulative score goes to zero or below, due to the accumulation of oneor more negative-scoring residue alignments; or the end of eithersequence is reached. The BLAST algorithm parameters W, T, and Xdetermine the sensitivity and speed of the alignment. The BLASTN program(for nucleotide sequences) uses as defaults a wordlength (W) of 11, anexpectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison ofboth strands. For amino acid sequences, the BLASTP program uses asdefaults a wordlength (W) of 3, an expectation (E) of 10, and theBLOSUM62 scoring matrix (see Henikoff & Henikoff (1989) Proc. Natl.Acad. Sci. USA 89:10915).

In addition to calculating percent sequence identity, the BLASTalgorithm also performs a statistical analysis of the similarity betweentwo sequences (see, e.g., Karlin & Altschul, Proc. Natl. Acad. Sci. USA90:5873-5787 (1993)). One measure of similarity provided by the BLASTalgorithm is the smallest sum probability (P(N)), which provides anindication of the probability by which a match between two nucleotide oramino acid sequences would occur by chance.

BLAST searches assume that proteins can be modeled as random sequences.However, many real proteins comprise regions of nonrandom sequenceswhich may be homopolymeric tracts, short-period repeats, or regionsenriched in one or more amino acids. Such low-complexity regions may bealigned between unrelated proteins even though other regions of theprotein are entirely dissimilar. A number of low-complexity filterprograms can be employed to reduce such low-complexity alignments. Forexample, the SEG (Wooten and Federhen, Comput. Chem., 17:149-163 (1993))and XNU (Claverie and States, Comput. Chem., 17:191-201 (1993))low-complexity filters can be employed alone or in combination.

(c) As used herein, “sequence identity” or “identity” in the context oftwo nucleic acid or polypeptide sequences includes reference to theresidues in the two sequences which are the same when aligned formaximum correspondence over a specified comparison window. Whenpercentage of sequence identity is used in reference to proteins it isrecognized that residue positions which are not identical often differby conservative amino acid substitutions, where amino acid residues aresubstituted for other amino acid residues with similar chemicalproperties (e.g. charge or hydrophobicity) and therefore do not changethe functional properties of the molecule. Where sequences differ inconservative substitutions, the percent sequence identity may beadjusted upwards to correct for the conservative nature of thesubstitution. Sequences which differ by such conservative substitutionsare said to have “sequence similarity” or “similarity”. Means for makingthis adjustment are well-known to those of skill in the art. Typicallythis involves scoring a conservative substitution as a partial ratherthan a full mismatch, thereby increasing the percentage sequenceidentity. Thus, for example, where an identical amino acid is given ascore of 1 and a non-conservative substitution is given a score of zero,a conservative substitution is given a score between zero and 1. Thescoring of conservative substitutions is calculated, e.g., according tothe algorithm of Meyers and Miller, Computer Applic. Biol. Sci., 4:11-17(1988) e.g., as implemented in the program PC/GENE (Intelligenetics,Mountain View, Calif., USA).

(d) As used herein, “percentage of sequence identity” means the valuedetermined by comparing two optimally aligned sequences over acomparison window, wherein the portion of the polynucleotide sequence inthe comparison window may comprise additions or deletions (i.e., gaps)as compared to the reference sequence (which does not comprise additionsor deletions) for optimal alignment of the two sequences. The percentageis calculated by determining the number of positions at which theidentical nucleic acid base or amino acid residue occurs in bothsequences to yield the number of matched positions, dividing the numberof matched positions by the total number of positions in the window ofcomparison and multiplying the result by 100 to yield the percentage ofsequence identity.

(e) The term “substantial identity” of polynucleotide sequences meansthat a polynucleotide comprises a sequence that has at least 70%sequence identity, preferably at least 80%, more preferably at least 90%and most preferably at least 95%, compared to a reference sequence usingone of the alignment programs described using standard parameters. Oneof skill will recognize that these values can be appropriately adjustedto determine corresponding identity of proteins encoded by twonucleotide sequences by taking into account codon degeneracy, amino acidsimilarity, reading frame positioning and the like. Substantial identityof amino acid sequences for these purposes normally means sequenceidentity of at least 60%, or preferably at least 70%, 80%, 90%, and mostpreferably at least 95%.

Another indication that nucleotide sequences are substantially identicalis if two molecules hybridize to each other under stringent conditions.However, nucleic acids which do not hybridize to each other understringent conditions are still substantially identical if thepolypeptides which they encode are substantially identical. This mayoccur, e.g., when a copy of a nucleic acid is created using the maximumcodon degeneracy permitted by the genetic code. One indication that twonucleic acid sequences are substantially identical is that thepolypeptide which the first nucleic acid sequence encodes isimmunologically cross reactive with the polypeptide encoded by thesecond nucleic acid sequence.

(e) The terms “substantial identity” in the context of a peptideindicates that a peptide comprises a sequence with at least 70% sequenceidentity to a reference sequence, preferably 80%, or preferably 85%,most preferably at least 90% or 95% sequence identity to the referencesequence over a specified comparison window. Optionally, optimalalignment is conducted using the homology alignment algorithm ofNeedleman and Wunsch, J. Mol. Biol. 48:443 (1970). An indication thattwo peptide sequences are substantially identical is that one peptide isimmunologically reactive with antibodies raised against the secondpeptide. Thus, a peptide is substantially identical to a second peptide,for example, where the two peptides differ only by a conservativesubstitution. Peptides which are “substantially similar” share sequencesas noted above except that residue positions which are not identical maydiffer by conservative amino acid changes.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIG. 1 shows the effects of water stress on wild-type and d1 plantsduring flowering and grain filling; mutant plants remain dark green andhealthy while wild-type plants dry out and have a few living leavesunder severe drought. The three watering conditions were: well-watered(100% soil relative water content), medium-water (45% soil relativewater content), and low water (30% soil relative water content)conditions. Photographs were taken 140-160 days after emergence.

FIG. 2 shows leaf temperatures on plants 165 days after emergence weremeasured by infrared thermography using a FLIR T620 Thermal ImagingCamera (FLIR Systems, USA). In order to obtain reliable comparisons,images were obtained over the shortest time interval possible;approximately 15 minutes total. Pseudo-colored temperature scales areindicated directly on the photographs.

FIG. 3 shows that net photosynthesis and stomatal conductance measuredon leaves between 120 and 130 days after emergence, using a Li-Cor 6400Portable Photosynthesis System. Light intensity was 500 μmol m⁻²s⁻¹.

FIG. 4 shows the relationship between stomatal conductance andtranspiration, measured under ambient conditions of 500 μmol m⁻²s⁻¹light intensity and 30° C. temperature using a Li-Cor 6400 PortablePhotosynthesis System. Measurements were taken on seedlings at 40 daysafter emergence. Each data point represents an individual plant. Linesdepicted are regression lines for each genotype; ANCOVA analysisdemonstrated significant differences (P<0.05) in the slopes.

FIG. 5 shows ψ_(leaf) measurements, which were made using a Scholanderpressure chamber. Measurements were taken on the flag leaf of theprimary tiller of plants 120-130 days after emergence.

FIG. 6 is a graph showing the percentage of stalks flowering at the endof the reproductive phase in high water, medium water, and low waterconditions.

FIG. 7 shows the average number of panicles produced through time in d1and wild-type plants.

FIG. 8 shows the percentage of grain viability at the end of thereproductive cycle under high water, medium water and low waterconditions. Data were obtained from 6 panicles randomly selected foranalysis from 6 different plants of each genotype and water treatmentcombination, measured at the end of the life cycle.

FIG. 9 is graph of yield of d1 and WT in well watered, medium water andlow water conditions.

FIG. 10 shows net photosynthesis and stomatal conductance at 1500 μmolm⁻²s⁻¹ light measured on the flag leaf of the primary tiller at 60 daysafter emergence using a Li-Cor 6400 Portable Photosynthesis System.

FIG. 11 shows that high planting density compromises plant growth andsurvival (as indicated by plant height) earlier in wild-type than in d1plants.

FIGS. 12A-B is a sequence alignment of the coding region of rgal and thed1 allele. (SEQ ID NO: 1 and 2 respectively).

FIG. 13 is a sequence alignment of the encoded proteins of rgal and thed1 allele. (SEQ ID NO: 3 and 4 respectively).

FIGS. 14A-D is a sequence alignment of the genomic region of rgal andthe d1 allele. (SEQ ID NO: 5 and 6 respectively).

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The rice dwarf mutant, d1, contains a non-functional RGA1 gene, encodingthe GTP-binding α-subunit of the heterotrimeric G protein. This mutantwas originally isolated as a spontaneous mutant with reduced height andshorter, erect, thicker, broad, dark green leaves, compact panicles, andshort, round grains. Applicants have identified that a non-functionalRGA1 gene or other related G-proteins can be used to create higher seedproduction and yield under drought conditions.

Thus the present invention provides for compositions and methods forproducing plants that have higher yield in drought conditions bymanipulating the G-proteins such as the RGA1 gene or protein. Inparticular, the present invention provides for plants, varieties, lines,and hybrids, as well as plant tissues and plant seeds that containmodified G-protein activity, particularly RGA1 activity to engineerdrought tolerance and improved seed production in plants.

In one embodiment, the present invention provides for one or more plantswhose germplasm has been modified to render a G-protein, particularlythe RGA1 gene or its gene product inactive. Moreover, in furtherembodiments the invention relates to the offspring (e.g., F1, F2, F3,etc.) of a cross of said plant wherein the germplasm of said offspringhas the same mutation as the parent plant. Therefore, embodiments of thepresent invention provide for plant varieties/hybrids whose germplasmcontains a mutation, such that the phenotype of the plants isnon-functional RGA1 gene activity in drought conditions. In someembodiments, said offspring (e.g., F1, F2, F3, etc.) are the result of across between elite lines, at least one of which contains a germplasmcomprising a mutation that renders the G-protein such as RGA1 protein orgene of said plant inactive, particularly during drought.

In another embodiment, the present invention provides a method ofimproving seed development in drought conditions comprising inhibitingthe activity of a G-protein, such as RGA1 protein during droughtconditions.

In another embodiment, the present invention provides a hybrid plant,line or variety, wherein said plant hybrid, line or variety comprisesgermplasm comprising one or more mutations in a G-protein encoding gene,or the RGA1 gene such that the G-protein or RGA1 protein is inactiveduring drought conditions. This can be by use of a naturally occurringmutation such as the d1 mutant, or preferably by introduction anexpression cassette to said plant designed to reduce activity of theRGA1 or other related G-protein gene either constitutively or underdrought conditions.

In some embodiments, said plant hybrid, line or variety is created byintrogression of a plant germplasm that comprises said one or moremodifications for rendering a G-protein or RGA1 gene or its encodedprotein product inactive. In some embodiments, said plant hybrid, lineor variety is created by incorporation of a heterologous geneticconstruct comprising designed to inhibit or otherwise decrease G-proteinactivity, particularly during drought conditions.

In another embodiment, the present invention provides a method forproducing a plant hybrid, line or variety resistant to droughtconditions and with improved seed production compared to a wild typeplant under the same conditions comprising identifying a germplasm witha null G-protein or RGA1 modification, and introducing said germplasminto an elite plant hybrid, line or variety. In some embodiments, saidintroducing of said germplasm into said elite hybrid, line or variety isby introgression. In some embodiments, said introducing of saidgermplasm into said elite plant hybrid, line or variety is byintroduction of a heterologous genetic construct.

In yet another embodiment, the present invention provides a planthybrid, line or variety wherein the germplasm of said hybrid, line orvariety comprises drought tolerance with improved seed production.

In yet another embodiment, the present invention provides a method foridentifying plant lines resistant to drought comprising supplying anucleic acid sample from a plant, providing amplification primers foramplifying a region of a plant corresponding to a G-protein or RGA1nucleic acid sample, applying said amplification primers to said nucleicacid sample such that amplification of said region of said G-proteingene occurs, and identifying plants resistant to drought based on thepresence of one or more null mutations in said amplified nucleic acidsample.

In still another embodiment, the present invention provides for seedswherein said germplasm of said seeds comprises a modified G-protein orRGA1 gene such that said mutation confers improved seed production underdrought conditions.

In some embodiments, the present invention provides for a plant thatcomprises a heterologous nucleotide sequence that is at least 70%homologous, at least 80% homologous, at least 85% homologous, at least90% homologous, at least 95% homologous, at least 97% homologous, or atleast 99% homologous to the RGA1 gene of SEQ ID NO:1, 2, 5, or 6. Theinvention also includes RGA1 polypeptides including the amino acidsequences of SEQ ID NO: 3 or 4, conservatively modified variants whichretain activity or loss of activity thereof as applicable.

In one embodiment, the present invention provides a method of producingplant seed comprising crossing a plant comprising a genetically modifiedG-protein or RGA1 gene with itself or a second plant and collecting saidseed from said cross. In some embodiments, the methods for producingsaid seed comprises planting a parent seed line wherein said parent seedline comprises a germplasm confers a decrease in activity or a G-proteinor RGA1 mutation with a parent pollinator plant line wherein saidpollinator and/or seed line germplasm comprises a germplasm that confersa modified G-protein of RGA1 protein, growing said parent seed andpollinator plants together, allowing for the said parent seed plants tobe pollinated by said parent pollinator plants, and harvesting the seedthat results from said pollination.

In yet another embodiment, the invention provides for geneticallymodified plants incorporating a heterologous nucleotide constructencoding a RGA1 gene such as SEQ ID NOS: 1, 2, 5, or 6 operably linkedto regulatory sequences such as expression cassettes, inhibitionconstructs, plants, plant cells, and seeds. The genetically modifiedplants, plant cells, and seeds of the invention may exhibit phenotypicchanges, such as modulated RGA1 activity, particularly during droughtconditions.

Methods are provided for reducing or eliminating the activity of aG-protein or RGA1 polypeptide in a plant, comprising introducing intothe plant a selected polynucleotide. In specific methods, providing thepolynucleotide decreases the level of RGA1 or related G-protein in theplant.

Methods are also provided for increasing the level of a modified RGA1 orG-protein polypeptide in a plant either constitutively or atspecifically regulated times and tissues comprising introducing into theplant a selected polynucleotide with appropriate regulatory elements. Inspecific methods, expression of the modified RGA1 or G-proteinpolynucleotide improves the plant's tolerance to drought.

Molecular Biology Techniques

The following is a non-limiting general overview of molecular biologytechniques which may be used in performing the methods of the invention.

Promoters

The constructs, promoters or control systems used in the methods of theinvention may include a tissue specific promoter, an inducible promoteror a constitutive promoter.

A large number of suitable promoter systems are available. For exampleone constitutive promoter useful for the invention is the cauliflowermosaic virus (CaMV) 35S. It has been shown to be highly active in manyplant organs and during many stages of development when integrated intothe genome of transgenic plants and has been shown to confer expressionin protoplasts of both dicots and monocots.

Organ-specific promoters are also well known. For example, the E8promoter is only transcriptionally activated during tomato fruitripening, and can be used to target gene expression in ripening tomatofruit (Deikman and Fischer, EMBO J. (1988) 7:3315; Giovannoni et al.,The Plant Cell (1989) 1:53). The activity of the E8 promoter is notlimited to tomato fruit, but is thought to be compatible with any systemwherein ethylene activates biological processes. Similarly theLipoxegenase (“the LOX gene”) is a fruit specific promoter.

Other fruit specific promoters are the 1.45 promoter fragment disclosedin Bird, et al., Plant Mol. Bio., pp 651-663(1988) and thepolygalacturonase promoter from tomato disclosed in U.S. Pat. No.5,413,937 to Bridges et al.

Leaf specific promoters include as the AS-1 promoter disclosed in U.S.Pat. No. 5,256,558 to Coruzzi and the RBCS-3A promoter isolated from peathe RBCS-3A gene disclosed in U.S. Pat. No. 5,023,179 to Lam et al.

And finally root specific promoters include the CamV 35S promoterdisclosed in U.S. Pat. No. 391,725 to Coruzzi et al; the RB7 promoterdisclosed in U.S. Pat. No. 5,459,252 to Conking et al. and the promoterisolated from Brassica napus disclosed in U.S. Pat. No. 5,401,836 toBazczynski et al. which give root specific expression.

Other examples of promoters include maternal tissue promoters such asseed coat, pericarp and ovule. Promoters highly expressed early inendosperm development are most effective in this application. Ofparticular interest is the promoter from the a′ subunit of the soybeanβ-conglycinin gene [Walling et al., Proc. Natl. Acad. Sci. USA83:2123-2127 (1986)] which is expressed early in seed development in theendosperm and the embryo.

Further seed specific promoters include the Napin promoter described inU.S. Pat. No. 5,110,728 to Calgene, which describes and discloses theuse of the napin promoter in directing the expression to seed tissue ofan acyl carrier protein to enhance seed oil production; the DC3 promoterfrom carrots which is early to mid embryo specific and is disclosed atPlant Physiology, October 1992 100(2) p. 576-581, “Hormonal andEnvironmental Regulation of the Carrot Lea-class Gene Dc 3, and PlantMol. Biol., April 1992, 18(6) p. 1049-1063, “Transcriptional Regulationof a Seed Specific Carrot Gene, DC 8”: the phaseolin promoter describedin U.S. Pat. No. 5,504,200 to Mycogen which discloses the gene sequenceand regulatory regions for phaseolin, a protein isolated from P.vulgaris which is expressed only while the seed is developing within thepod, and only in tissues involved in seed generation.

Other organ-specific promoters appropriate for a desired target organcan be isolated using known procedures. These control sequences aregenerally associated with genes uniquely expressed in the desired organ.In a typical higher plant, each organ has thousands of mRNAs that areabsent from other organ systems (reviewed in Goldberg, Phil, Trans. R.Soc. London (1986) B314-343. mRNAs are first isolated to obtain suitableprobes for retrieval of the appropriate genomic sequence which retainsthe presence of the natively associated control sequences. An example ofthe use of techniques to obtain the cDNA associated with mRNA specificto avocado fruit is found in Christoffersen et al., Plant MolecularBiology (1984) 3:385. Briefly, mRNA was isolated from ripening avocadofruit and used to make a cDNA library. Clones in the library wereidentified that hybridized with labeled RNA isolated from ripeningavocado fruit, but that did not hybridize with labeled RNAs isolatedfrom unripe avocado fruit. Many of these clones represent mRNAs encodedby genes that are transcriptionally activated at the onset of avocadofruit ripening.

Another very important method that can be used to identify cell typespecific promoters that allow identification of genes expressed even ina single cell is enhancer detection (O'Kane, C., and Gehring, W. J.(1987), “Detection in situ of genomic regulatory elements inDrosophila”, Proc. Natl. Acad. Sci. USA, 84, 9123-9127). This method wasfirst developed in Drosophila and rapidly adapted to mice and plants(Wilson, C., Pearson, R. K., Bellen, H. J., O'Kane, C. J., Grossniklaus,U., and Gehring, W. J. (1989)), “P-element-mediated enhancer detection:an efficient method for isolating and characterizing developmentallyregulated genes in Drosophila”, Genes & Dev., 3, 1301-1313; Skarnes, W.C. (1990), “Entrapment vectors: a new tool for mammalian genetics”,Biotechnology, 8, 827-831; Topping, J. F., Wei, W., and Lindsey, K.(1991), “Functional tagging of regulatory elements in the plant genome”,Development, 112, 1009-1019; Sundaresan, V., Springer, P. S., Volpe, T.,Haward, S., Jones, J. D. G., Dean, C., Ma, H., and Martienssen, R. A.,(1995), “Patterns of gene action in plant development revealed byenhancer trap and gene trap transposable elements”, Genes & Dev., 9,1797-1810).

The promoter used in the method of the invention may be an induciblepromoter. An inducible promoter is a promoter that is capable ofdirectly or indirectly activating transcription of a DNA sequence inresponse to an inducer. In the absence of an inducer, the DNA sequencewill not be transcribed. Typically, the protein factor that bindsspecifically to an inducible promoter to activate transcription ispresent in an inactive form which is then directly or indirectlyconverted to the active form by the inducer. The inducer may be achemical agent such as a protein, metabolite (sugar, alcohol etc.), agrowth regulator, herbicide, or a phenolic compound or a physiologicalstress imposed directly by heat, salt, toxic elements etc. or indirectlythrough the action of a pathogen or disease agent such as a virus. Aplant cell containing an inducible promoter may be exposed to an inducerby externally applying the inducer to the cell such as by spraying,watering, heating, or similar methods. Examples of inducible promotersinclude the inducible 70 kD heat shock promoter of (Freeling, M.,Bennet, D. C., Maize ADN 1, Ann. Rev. of Genetics, 19:297-323) and thealcohol dehydrogenase promoter which is induced by ethanol (Nagao, R.T., et al., Miflin, B. J., Ed. Oxford Surveys of Plant Molecular andCell Biology, Vol. 3, p. 384-438, Oxford University Press, Oxford 1986)or the Lex A promoter which is triggered with chemical treatment and isavailable through Ligand Pharmaceuticals. The inducible promoter may bein an induced state throughout seed formation or at least for a periodwhich corresponds to the transcription of the DNA sequence of therecombinant DNA molecule(s).

Another example of an inducible promoter is the chemically induciblegene promoter sequence isolated from a 27 kD subunit of the maizeglutathione-S-transferase (GST II) gene. Two of the inducers for thispromoter are N,N-diallyl-2,2-dichloroacetamide (common name:dichloramid) orbenzyl-=2-chloro-4-(trifluoromethyl)-5-thiazolecarboxylate (common name:flurazole). In addition, a number of other potential inducers may beused with this promoter as described in published PCT Application No.PCT/GB90/00110 by ICI.

Another example of an inducible promoter is the light induciblechlorophyll a/b binding protein (CAB) promoter, also described inpublished PCT Application No. PCT/GB90/00110 by ICI.

Inducible promoters have also been described in published ApplicationNo. EP89/103888.7 by Ciba-Geigy. In this application, a number ofinducible promoters are identified, including the PR protein genes,especially the tobacco PR protein genes, such as PR-1a, PR-1b, PR-1c,PR-1, PR-A, PR-S, the cucumber chitinase gene, and the acidic and basictobacco beta-1,3-glucanase genes. There are numerous potential inducersfor these promoters, as described in Application No. EP89/103888.7.

The preferred promoters may be used in conjunction with naturallyoccurring flanking coding or transcribed sequences of the feroniaregulatory genes or with any other coding or transcribed sequence thatis critical to pollen tube formation and/or fertilization.

It may also be desirable to include some intron sequences in thepromoter constructs since the inclusion of intron sequences in thecoding region may result in enhanced expression and specificity. Thus,it may be advantageous to join the DNA sequences to be expressed to apromoter sequence that contains the first intron and exon sequences of apolypeptide which is unique to cells/tissues of a plant critical tofemale gametophyte development and/or function.

Additionally, regions of one promoter may be joined to regions from adifferent promoter in order to obtain the desired promoter activityresulting in a chimeric promoter. Synthetic promoters which regulategene expression may also be used.

The expression system may be further optimized by employing supplementalelements such as transcription terminators and/or enhancer elements.

Other Regulatory Elements

In addition to a promoter sequence, an expression cassette or constructshould also contain a transcription termination region downstream of thestructural gene to provide for efficient termination. The terminationregion or polyadenylation signal may be obtained from the same gene asthe promoter sequence or may be obtained from different genes.Polyadenylation sequences include, but are not limited to theAgrobacterium octopine synthase signal (Gielen et al., EMBO J. (1984)3:835-846) or the nopaline synthase signal (Depicker et al., Mol. andAppl. Genet. (1982) 1:561-573).

Marker Genes

Recombinant DNA molecules containing any of the DNA sequences andpromoters described herein may additionally contain selection markergenes which encode a selection gene product which confer on a plant cellresistance to a chemical agent or physiological stress, or confers adistinguishable phenotypic characteristic to the cells such that plantcells transformed with the recombinant DNA molecule may be easilyselected using a selective agent. One such selection marker gene isneomycin phosphotransferase (NPT II) which confers resistance tokanamycin and the antibiotic G-418. Cells transformed with thisselection marker gene may be selected for by assaying for the presencein vitro of phosphorylation of kanamycin using techniques described inthe literature or by testing for the presence of the mRNA coding for theNPT II gene by Northern blot analysis in RNA from the tissue of thetransformed plant. Polymerase chain reactions are also used to identifythe presence of a transgene or expression using reverse transcriptasePCR amplification to monitor expression and PCR on genomic DNA. Othercommonly used selection markers include the ampicillin resistance gene,the tetracycline resistance and the hygromycin resistance gene.Transformed plant cells thus selected can be induced to differentiateinto plant structures which will eventually yield whole plants. It is tobe understood that a selection marker gene may also be native to aplant.

Transformation

Numerous methods for plant transformation have been developed, includingbiological and physical, plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glick,B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages67-88. In addition, expression vectors and in vitro culture methods forplant cell or tissue transformation and regeneration of plants areavailable. See, for example, Gruber et al., “Vectors for PlantTransformation” in Methods in Plant Molecular Biology and Biotechnology,Glick, B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton,1993) pages 89-119.

A. Agrobacterium-Mediated Transformation

One method for introducing an expression vector into plants is based onthe natural transformation system of Agrobacterium. See, for example,Horsch et al., Science 227: 1229 (1985). A. tumefaciens and A.rhizogenes are plant pathogenic soil bacteria which geneticallytransform plant cells. The Ti and Ri plasmids of A. tumefaciens and A.rhizogenes, respectively, carry genes responsible for genetictransformation of the plant. See, for example, Kado, C. I., Crit. Rev.Plant. Sci. 10: 1 (1991). Descriptions of Agrobacterium vector systemsand methods for Agrobacterium-mediated gene transfer are provided byGruber et al., supra, Miki et al., supra, and Moloney et al., Plant CellReports 8: 238 (1989). See also, U.S. Pat. No. 5,563,055, (Townsend andThomas), issued Oct. 8, 1996.

B. Direct Gene Transfer

Several methods of plant transformation, collectively referred to asdirect gene transfer, have been developed as an alternative toAgrobacterium-mediated transformation. A generally applicable method ofplant transformation is microprojectile-mediated transformation whereinDNA is carried on the surface of microprojectiles measuring 1 to 4 μm.The expression vector is introduced into plant tissues with a biolisticdevice that accelerates the microprojectiles to speeds of 300 to 600 m/swhich is sufficient to penetrate plant cell walls and membranes. Sanfordet al., Part. Sci. Technol. 5: 27 (1987), Sanford, J. C., TrendsBiotech. 6: 299 (1988), Klein et al., Bio/Technology 6: 559-563 (1988),Sanford, J. C., Physiol Plant 79: 206 (1990), Klein et al.,Biotechnology 10: 268 (1992). See also U.S. Pat. No. 5,015,580(Christou, et al), issued May 14, 1991; U.S. Pat. No. 5,322,783 (Tomes,et al.), issued Jun. 21, 1994.

Another method for physical delivery of DNA to plants is sonication oftarget cells. Zhang et al., Bio/Technology 9: 996 (1991). Alternatively,liposome or spheroplast fusion have been used to introduce expressionvectors into plants. Deshayes et al., EMBO 1, 4: 2731 (1985), Christouet al., Proc Natl. Acad. Sci. U.S.A. 84: 3962 (1987). Direct uptake ofDNA into protoplasts using CaCl₂ precipitation, polyvinyl alcohol orpoly-L-ornithine have also been reported. Hain et al., Mol. Gen. Genet.199: 161 (1985) and Draper et al., Plant Cell Physiol. 23: 451 (1982).Electroporation of protoplasts and whole cells and tissues have alsobeen described. Donn et al., In Abstracts of VIIth InternationalCongress on Plant Cell and Tissue Culture IAPTC, A2-38, p 53 (1990);D'Halluin et al., Plant Cell 4: 1495-1505 (1992) and Spencer et al.,Plant Mol. Biol. 24: 51-61 (1994).

Following transformation of target tissues, expression of theabove-described selectable marker genes allows for preferentialselection of transformed cells, tissues and/or plants, usingregeneration and selection methods now well known in the art.

It is often desirable to have the DNA sequence in homozygous state whichmay require more than one transformation event to create a parentalline, requiring transformation with a first and second recombinant DNAmolecule both of which encode the same gene product. It is furthercontemplated in some of the embodiments of the process of the inventionthat a plant cell be transformed with a recombinant DNA moleculecontaining at least two DNA sequences or be transformed with more thanone recombinant DNA molecule. The DNA sequences or recombinant DNAmolecules in such embodiments may be physically linked, by being in thesame vector, or physically separate on different vectors. A cell may besimultaneously transformed with more than one vector provided that eachvector has a unique selection marker gene. Alternatively, a cell may betransformed with more than one vector sequentially allowing anintermediate regeneration step after transformation with the firstvector. Further, it may be possible to perform a sexual cross betweenindividual plants or plant lines containing different DNA sequences orrecombinant DNA molecules preferably the DNA sequences or therecombinant molecules are linked or located on the same chromosome, andthen selecting from the progeny of the cross, plants containing both DNAsequences or recombinant DNA molecules.

Expression of recombinant DNA molecules containing the DNA sequences andpromoters described herein in transformed plant cells may be monitoredusing Northern blot techniques and/or Southern blot techniques known tothose of skill in the art.

The transformed cells may then be regenerated into a transgenic plant.The regenerated plants are transferred to standard soil conditions andcultivated in a conventional manner.

After the expression or inhibition cassette is stably incorporated intoregenerated transgenic plants, it can be transferred to other plants bysexual crossing. Any of a number of standard breeding techniques can beused, depending upon the species to be crossed. It may be useful togenerate a number of individual transformed plants with any recombinantconstruct in order to recover plants free from any position effects. Itmay also be preferable to select plants that contain more than one copyof the introduced recombinant DNA molecule such that high levels ofexpression of the recombinant molecule are obtained.

As indicated above, it may be desirable to produce plant lines which arehomozygous for a particular gene. In some species this is accomplishedrather easily by the use of another culture or isolated microsporeculture. This is especially true for the oil seed crop Brassica napus(Keller and Armstrong, Z. Pflanzenzucht 80:100-108, 1978). By usingthese techniques, it is possible to produce a haploid line that carriesthe inserted gene and then to double the chromosome number eitherspontaneously or by the use of colchicine. This gives rise to a plantthat is homozygous for the inserted gene, which can be easily assayedfor if the inserted gene carries with it a suitable selection markergene for detection of plants carrying that gene. Alternatively, plantsmay be self-fertilized, leading to the production of a mixture of seedthat consists of, in the simplest case, three types, homozygous (25%),heterozygous (50%) and null (25%) for the inserted gene. Although it isrelatively easy to score null plants from those that contain the gene,it is possible in practice to score the homozygous from heterozygousplants by Southern blot analysis in which careful attention is paid tothe loading of exactly equivalent amounts of DNA from the mixedpopulation, and scoring heterozygotes by the intensity of the signalfrom a probe specific for the inserted gene. It is advisable to verifythe results of the Southern blot analysis by allowing each independenttransformant to self-fertilize, since additional evidence forhomozygosity can be obtained by the simple fact that if the plant washomozygous for the inserted gene, all of the subsequent plants from theselfed seed will contain the gene, while if the plant was heterozygousfor the gene, the generation grown from the selfed seed will containnull plants. Therefore, with simple selfing one can easily selecthomozygous plant lines that can also be confirmed by southern blotanalysis.

Creation of homozygous parental lines makes possible the production ofhybrid plants and seeds which will contain a modified protein component.Transgenic homozygous parental lines are maintained with each parentcontaining either the first or second recombinant DNA sequence operablylinked to a promoter. Also incorporated in this scheme are theadvantages of growing a hybrid crop, including the combining of morevaluable traits and hybrid vigor.

The nucleotide constructs of the invention also encompass nucleotideconstructs that may be employed in methods for altering or mutating agenomic nucleotide sequence in an organism, including, but not limitedto, chimeric vectors, chimeric mutational vectors, chimeric repairvectors, mixed-duplex oligonucleotides, self-complementary chimericoligonucleotides, and recombinogenic oligonucleobases. Such nucleotideconstructs and methods of use, such as, for example, chimeraplasty, areknown in the art. Chimeraplasty involves the use of such nucleotideconstructs to introduce site-specific changes into the sequence ofgenomic DNA within an organism. See, U.S. Pat. Nos. 5,565,350;5,731,181; 5,756,325; 5,760,012; 5,795,972; and 5,871,984; all of whichare herein incorporated by reference. See also, WO 98/49350, WO99/07865, WO 99/25821, and Beetham et al. (1999) Proc. Natl. Acad. Sci.USA 96:8774-8778; herein incorporated by reference.

Molecular Markers

The present invention provides a method of genotyping a plant comprisinga heterologous polynucleotide of the present invention. Genotypingprovides a means of distinguishing homologs of a chromosome pair and canbe used to differentiate segregants in a plant population. Molecularmarker methods can be used for phylogenetic studies, characterizinggenetic relationships among crop varieties, identifying crosses orsomatic hybrids, localizing chromosomal segments affecting monogenictraits, map based cloning, and the study of quantitative inheritance.See, e.g., Clark, Ed., Plant Molecular Biology: A Laboratory Manual.Berlin, Springer Verlag, 1997. Chapter 7. For molecular marker methods,see generally, “The DNA Revolution” in: Paterson, A. H., Genome Mappingin Plants (Austin, Tex., Academic Press/R. G. Landis Company, 1996) pp.7-21.

The particular method of genotyping in the present invention may employany number of molecular marker analytic techniques such as, but notlimited to, restriction fragment length polymorphisms (RFLPs). RFLPs arethe product of allelic differences between DNA restriction fragmentsresulting from nucleotide sequence variability. As is well known tothose of skill in the art, RFLPs are typically detected by extraction ofgenomic DNA and digestion with a restriction enzyme. Generally, theresulting fragments are separated according to size and hybridized witha probe; single copy probes are preferred. Restriction fragments fromhomologous chromosomes are revealed.

Differences in fragment size among alleles represent an RFLP. Thus, thepresent invention further provides a means to follow segregation of agene or nucleic acid of the present invention as well as chromosomalsequences genetically linked to these genes or nucleic acids using suchtechniques as RFLP analysis. Linked chromosomal sequences are within 50centiMorgans (cM), often within 40 or 30 cM, preferably within 20 or 10cM, more preferably within 5, 3, 2, or 1 cM of a gene of the presentinvention.

In the present invention, the nucleic acid probes employed for molecularmarker mapping of plant nuclear genomes selectively hybridize, underselective hybridization conditions, to a gene encoding a polynucleotideof the present invention. In preferred embodiments, the probes areselected from polynucleotides of the present invention.

Typically, these probes are cDNA probes or restriction-enzyme treated(e.g., Pst I) genomic clones. The length of the probes is discussed ingreater detail, supra, but are typically at least 15 bases in length,more preferably at least 20, 25, 30, 35, 40, or 50 bases in length.Generally, however, the probes are less than about 1 kilobase in length.Preferably, the probes are single copy probes that hybridize to a uniquelocus in a haploid chromosome complement. Some exemplary restrictionenzymes employed in RFLP mapping are EcoRI, EcoRv, and SstI. As usedherein the term “restriction enzyme” includes reference to a compositionthat recognizes and, alone or in conjunction with another composition,cleaves at a specific nucleotide sequence.

The method of detecting an RFLP comprises the steps of (a) digestinggenomic DNA of a plant with a restriction enzyme; (b) hybridizing anucleic acid probe, under selective hybridization conditions, to asequence of a polynucleotide of the present of said genomic DNA; (c)detecting therefrom a RFLP. Other methods of differentiating polymorphic(allelic) variants of polynucleotides of the present invention can behad by utilizing molecular marker techniques well known to those ofskill in the art including such techniques as: 1) single strandedconformation analysis (SSCA); 2) denaturing gradient gel electrophoresis(DGGE); 3) RNase protection assays; 4) allele-specific oligonucleotides(ASOs); 5) the use of proteins which recognize nucleotide mismatches,such as the E. coli mutS protein; and 6) allele-specific PCR. Otherapproaches based on the detection of mismatches between the twocomplementary DNA strands include clamped denaturing gel electrophoresis(CDGE); heteroduplex analysis (HA); and chemical mismatch cleavage(CMC). Thus, the present invention further provides a method ofgenotyping comprising the steps of contacting, under stringenthybridization conditions, a sample suspected of comprising apolynucleotide of the present invention with a nucleic acid probe.Generally, the sample is a plant sample; preferably, a sample suspectedof comprising a maize polynucleotide of the present invention (e.g.,gene, mRNA). The nucleic acid probe selectively hybridizes, understringent conditions, to a subsequence of a polynucleotide of thepresent invention comprising a polymorphic marker. Selectivehybridization of the nucleic acid probe to the polymorphic markernucleic acid sequence yields a hybridization complex. Detection of thehybridization complex indicates the presence of that polymorphic markerin the sample. In preferred embodiments, the nucleic acid probecomprises a polynucleotide of the present invention.

UTRs and Codon Preference

In general, translational efficiency has been found to be regulated byspecific sequence elements in the 5′ non-coding or untranslated region(5′UTR) of the RNA. Positive sequence motifs include translationalinitiation consensus sequences (Kozak, Nucleic Acids Res. 15: 8125(1987)) and the 7-methylguanosine cap structure (Drummond et al.,Nucleic Acids Res. 13: 7375 (1985)). Negative elements include stableintramolecular 5′ UTR stem-loop structures (Muesing et al., Cell 48: 691(1987)) and AUG sequences or short open reading frames preceded by anappropriate AUG in the 5 ‘UTR (Kozak, supra, Rao et al., Mol. and Cell.Biol. 8: 284 (1988)). Accordingly, the present invention provides 5’and/or 3′ untranslated regions for modulation of translation ofheterologous coding sequences.

Further, the polypeptide-encoding segments of the polynucleotides of thepresent invention can be modified to alter codon usage. Altered codonusage can be employed to alter translational efficiency and/or tooptimize the coding sequence for expression in a desired host such as tooptimize the codon usage in a heterologous sequence for expression inmaize. Codon usage in the coding regions of the polynucleotides of thepresent invention can be analyzed statistically using commerciallyavailable software packages such as “Codon Preference” available fromthe University of Wisconsin Genetics Computer Group (see Devereaux etal., Nucleic Acids Res. 12: 387-395 (1984)) or MacVector 4.1 (EastmanKodak Co., New Haven, Conn.). Thus, the present invention provides acodon usage frequency characteristic of the coding region of at leastone of the polynucleotides of the present invention. The number ofpolynucleotides that can be used to determine a codon usage frequencycan be any integer from 1 to the number of polynucleotides of thepresent invention as provided herein. Optionally, the polynucleotideswill be full-length sequences. An exemplary number of sequences forstatistical analysis can be at least 1, 5, 10, 20, 50, or 100.

Sequence Shuffling

The present invention provides methods for sequence shuffling usingpolynucleotides of the present invention, and compositions resultingtherefrom. Sequence shuffling is described in PCT publication No. WO97/20078. See also, Zhang, J.-H., et al. Proc. Natl. Acad. Sci. USA 94:4504-4509 (1997). Generally, sequence shuffling provides a means forgenerating libraries of polynucleotides having a desired characteristicwhich can be selected or screened for. Libraries of recombinantpolynucleotides are generated from a population of related sequencepolynucleotides which comprise sequence regions which have substantialsequence identity and can be homologously recombined in vitro or invivo. The population of sequence-recombined polynucleotides comprises asubpopulation of polynucleotides which possess desired or advantageouscharacteristics and which can be selected by a suitable selection orscreening method. The characteristics can be any property or attributecapable of being selected for or detected in a screening system, and mayinclude properties of: an encoded protein, a transcriptional element, asequence controlling transcription, RNA processing, RNA stability,chromatin conformation, translation, or other expression property of agene or transgene, a replicative element, a protein-binding element, orthe like, such as any feature which confers a selectable or detectableproperty. In some embodiments, the selected characteristic will be adecreased Km and/or increased KCat over the wild-type protein asprovided herein. In other embodiments, a protein or polynucleotidegenerated from sequence shuffling will have a ligand binding affinitygreater than the non-shuffled wild-type polynucleotide. The increase insuch properties can be at least 110%, 120%, 130%, 140% or at least 150%of the wild-type value.

Generic and Consensus Sequences

Polynucleotides and polypeptides of the present invention furtherinclude those having: (a) a generic sequence of at least two homologouspolynucleotides or polypeptides, respectively, of the present invention;and, (b) a consensus sequence of at least three homologouspolynucleotides or polypeptides, respectively, of the present invention.The generic sequence of the present invention comprises each species ofpolypeptide or polynucleotide embraced by the generic polypeptide orpolynucleotide sequence, respectively. The individual speciesencompassed by a polynucleotide having an amino acid or nucleic acidconsensus sequence can be used to generate antibodies or produce nucleicacid probes or primers to screen for homologs in other species, genera,families, orders, classes, phyla, or kingdoms.

Alternatively, a polynucleotide having a consensus sequence generatedfrom orthologous genes can be used to identify or isolate orthologs ofother taxa. Typically, a polynucleotide having a consensus sequence willbe at least 25, 30, or 40 in nucleotides in length. As those of skill inthe art are aware, a conservative amino acid substitution can be usedfor amino acids which differ amongst aligned sequences but are from thesame conservative substitution group as discussed above. Optionally, nomore than 1 or 2 conservative amino acids are substituted for each 10amino acid length of consensus sequence.

Similar sequences used for generation of a consensus or generic sequenceinclude any number and combination of allelic variants of the same gene,orthologous, or paralogous sequences as provided herein. Optionally,similar sequences used in generating a consensus or generic sequence areidentified using the BLAST algorithm's smallest sum probability (P(N)).Various suppliers of sequence-analysis software are listed in chapter 7of Current Protocols in Molecular Biology, F. M. Ausubel et al., Eds.,Current Protocols, a joint venture between Greene Publishing Associates,Inc. and John Wiley & Sons, Inc. (Supplement 30).

A polynucleotide sequence is considered similar to a reference sequenceif the smallest sum probability in a comparison of the test nucleic acidto the reference nucleic acid is less than about 0.1, more preferablyless than about 0.01, or 0.001, and most preferably less than about0.0001, or 0.00001. Similar polynucleotides can be aligned and aconsensus or generic sequence generated using multiple sequencealignment software available from a number of commercial suppliers suchas the Genetics Computer Group's (Madison, Wis.) PILEUP software, VectorNTI's (North Bethesda, Md.) ALIGNX, or Genecode's (Ann Arbor, Mich.)SEQUENCHER. Conveniently, default parameters of such software can beused to generate consensus or generic sequences.

Reducing the Activity and/or Level of an RGA1 Polypeptide

Methods are also provided to reduce or eliminate the activity of an RGA1polypeptide by transforming a plant cell with an expression cassettethat expresses a polynucleotide that inhibits the expression of theRGA1. The polynucleotide may inhibit the expression of the RGA1directly, by preventing transcription or translation of the RGA1messenger RNA, or indirectly, by encoding a polypeptide that inhibitsthe transcription or translation of an RGA1 gene encoding an RGA1polypeptide. Methods for inhibiting or eliminating the expression of agene in a plant are well known in the art, and any such method may beused in the present invention to inhibit the expression of the RGA1polypeptide. Many methods may be used to reduce or eliminate theactivity of an RGA1 polypeptide. In addition, more than one method maybe used to reduce the activity of a single RGA1 polypeptide.

1. Polynucleotide-Based Methods:

In some embodiments of the present invention, a plant is transformedwith an expression cassette that is capable of expressing apolynucleotide that inhibits the expression of an RGA1 polypeptide ofthe invention. The term “expression” as used herein refers to thebiosynthesis of a gene product, including the transcription and/ortranslation of said gene product. For example, for the purposes of thepresent invention, an expression cassette capable of expressing apolynucleotide that inhibits the expression of at least one RGA1polypeptide is an expression cassette capable of producing an RNAmolecule that inhibits the transcription and/or translation of at leastone RGA1 polypeptide of the invention. The “expression” or “production”of a protein or polypeptide from a DNA molecule refers to thetranscription and translation of the coding sequence to produce theprotein or polypeptide, while the “expression” or “production” of aprotein or polypeptide from an RNA molecule refers to the translation ofthe RNA coding sequence to produce the protein or polypeptide.

Examples of polynucleotides that inhibit the expression of an RGA1polypeptide include sense Suppression/Cosuppression, where an expressioncassette is designed to express an RNA molecule corresponding to all orpart of a messenger RNA encoding an RGA1 polypeptide in the “sense”orientation and over expression of the RNA molecule can result inreduced expression of the native gene; Antisense Suppression where theexpression cassette is designed to express an RNA molecule complementaryto all or part of a messenger RNA encoding the RGA1 polypeptide and overexpression of the antisense RNA molecule can result in reducedexpression of the native gene; Double-Stranded RNA Interference, where asense RNA molecule like that described above for cosuppression and anantisense RNA molecule that is fully or partially complementary to thesense RNA molecule are expressed in the same cell, resulting ininhibition of the expression of the corresponding endogenous messengerRNA, Hairpin RNA Interference and Intron-Containing Hairpin RNAInterference.

Where the expression cassette is designed to express an RNA moleculethat hybridizes with itself to form a hairpin structure that comprises asingle-stranded loop region and a base-paired stem, Small InterferingRNA or Micro RNA, where the expression cassette is designed to expressan RNA molecule that is modeled on an endogenous miRNA such as smallinterfering RNA or artificial micro RNAs.

2. Polypeptide-Based Inhibition of Gene Expression

In one embodiment, the polynucleotide encodes a zinc finger protein thatbinds to a gene encoding an RGA1 polypeptide, resulting in reducedexpression of the gene methods of selecting sites for targeting by zincfinger proteins have been described, for example, in U.S. Pat. No.6,453,242, and methods for using zinc finger proteins to inhibit theexpression of genes in plants are described, for example, in U.S. PatentPublication No. 2003/0037355; each of which is herein incorporated byreference.

3. Polypeptide-Based Inhibition of Protein Activity

In some embodiments of the invention, the polynucleotide encodes anantibody that binds to at least one RGA1 polypeptide and reduces theactivity of the RGA1 polypeptide. The expression of antibodies in plantcells and the inhibition of molecular pathways by expression and bindingof antibodies to proteins in plant cells are well known in the art. See,for example, Conrad and Sonnewald, (2003) Nature Biotech. 21:35-36,incorporated herein by reference.

4. Gene Disruption

In some embodiments of the present invention, the activity of an RGA1polypeptide is reduced or eliminated by disrupting the gene encoding theRGA1 polypeptide. The gene encoding the RGA1 polypeptide may bedisrupted by any method known in the art. For example, in oneembodiment, the gene is disrupted by transposon tagging. In anotherembodiment, the gene is disrupted by mutagenizing plants using random ortargeted mutagenesis, and selecting for plants that have a desired traitor phenotype.

In certain embodiments the nucleic acid sequences of the presentinvention can be stacked with any combination of polynucleotidesequences of interest in order to create plants with a desiredphenotype. For example, the polynucleotides of the present invention maybe stacked with any other polynucleotides of the present invention, (SEQID NO: 1), or with other genes implicated in herbicide resistance. Thecombinations generated can also include multiple copies of any one ofthe polynucleotides of interest. The polynucleotides of the presentinvention can also be stacked with any other gene or combination ofgenes to produce plants with a variety of desired trait combinationsincluding but not limited to traits desirable for animal feed such ashigh oil genes (e.g., U.S. Pat. No. 6,232,529); balanced amino acids(e.g. hordothionins (U.S. Pat. Nos. 5,990,389; 5,885,801; 5,885,802; and5,703,409)); barley high lysine (Williamson et al. (1987) Eur. J.Biochem. 165:99-106; and WO 98/20122); and high methionine proteins(Pedersen et al. (1986) J. Biol. Chem. 261:6279; Kirihara et al. (1988)Gene 71:359; and Musumura et al. (1989) Plant Mol. Biol. 12: 123));increased digestibility (e.g., modified storage proteins (U.S.application Ser. No. 10/053,410, filed Nov. 7, 2001)); and thioredoxins(U.S. application Ser. No. 10/005,429, filed Dec. 3, 2001), thedisclosures of which are herein incorporated by reference.

The polynucleotides of the present invention can also be stacked withtraits desirable for insect, disease or herbicide resistance (e.g.,Bacillus thuringiensis toxic proteins (U.S. Pat. Nos. 5,366,892;5,747,450; 5,737,514; 5,723,756; 5,593,881; Geiser et al (1986) Gene48:109); lectins (Van Damme et al. (1994) Plant Mol. Biol. 24:825);fumonisin detoxification genes (U.S. Pat. No. 5,792,931); avirulence anddisease resistance genes (Jones et al. (1994) Science 266:789; Martin etal. (1993) Science 262:1432; Mindrinos et al. (1994) Cell 78:1089);acetolactate synthase (ALS) mutants that lead to herbicide resistancesuch as the S4 and/or Hra mutations; inhibitors of glutamine synthasesuch as phosphinothricin or basta (e.g., bar gene); and glyphosateresistance (EPSPS gene and GAT gene)); and traits desirable forprocessing or process products such as high oil (U.S. Pat. No.6,232,529); modified oils (e.g., fatty acid desaturase genes (U.S. Pat.No. 5,952,544; WO 94/11516)); modified starches (e.g., ADPGpyrophosphorylases (AGPase), starch synthases (SS), starch branchingenzymes (SBE) and starch debranching enzymes (SDBE)); and polymers orbioplastics (U.S. Pat. No. 5,602,321); beta-ketothiolase,polyhydroxybutyrate synthase, and acetoacetyl-CoA reductase (Schubert etal. (1988) J. Bacteriol. 170:5837-5847), which facilitate expression ofpolyhydroxyalkanoates (PHAs)), the disclosures of which are hereinincorporated by reference. One could also combine the polynucleotides ofthe present invention with polynucleotides providing agronomic traitssuch as male sterility (see U.S. Pat. No. 5,583,210), stalk strength,flowering time, or transformation technology traits such as cell cycleregulation or gene targeting (see, WO 99/61619; WO 00/17364; WO99/25821), the disclosures of which are herein incorporated byreference.

These stacked combinations can be created by any method including, butnot limited to, polynucleotide sequences of interest can be combined atany time and in any order. For example, a transgenic plant comprisingone or more desired traits can be used as the target to introducefurther traits by subsequent transformation. The traits can beintroduced simultaneously in a co-transformation protocol with thepolynucleotides of interest provided by any combination oftransformation cassettes. For example, if two sequences will beintroduced, the two sequences can be contained in separatetransformation cassettes (trans) or contained on the same transformationcassette (cis). Expression of the sequences can be driven by the samepromoter or by different promoters. In certain cases, it may bedesirable to introduce a transformation cassette that will suppress theexpression of the polynucleotide of interest. This may be combined withany combination of other suppression cassettes or overexpressioncassettes to generate the desired combination of traits in the plant.

Use in Breeding Methods

The transformed plants of the invention may be used in a plant breedingprogram. The goal of plant breeding is to combine, in a single varietyor hybrid, various desirable traits. For field crops, these traits mayinclude, for example, resistance to diseases and insects, tolerance toheat and drought, tolerance to high planting density, reduced time tocrop maturity, greater yield, and better agronomic quality. Withmechanical harvesting of many crops, uniformity of plant characteristicssuch as germination and stand establishment, growth rate, maturity, andplant height is desirable. Traditional plant breeding is an importanttool in developing new and improved commercial crops. This inventionencompasses methods for producing a plant by crossing a first parentplant with a second parent plant wherein one or both of the parentplants is a transformed plant according to the invention displayingdrought tolerance as described herein.

Plant breeding techniques known in the art and used in a plant breedingprogram include, but are not limited to, recurrent selection, bulkselection, mass selection, backcrossing, pedigree breeding, openpollination breeding, restriction fragment length polymorphism enhancedselection, genetic marker enhanced selection, doubled haploids, andtransformation. Often combinations of these techniques are used.

The development of hybrids in a plant breeding program requires, ingeneral, the development of homozygous inbred lines, the crossing ofthese lines, and the evaluation of the crosses. There are manyanalytical methods available to evaluate the result of a cross. Theoldest and most traditional method of analysis is the observation ofphenotypic traits. Alternatively, the genotype of a plant can beexamined.

A genetic trait which has been engineered into a particular plant usingtransformation techniques can be moved into another line usingtraditional breeding techniques that are well known in the plantbreeding arts. For example, a backcrossing approach is commonly used tomove a transgene from a transformed maize plant to an elite inbred line,and the resulting progeny would then comprise the transgene(s). Also, ifan inbred line was used for the transformation, then the transgenicplants could be crossed to a different inbred in order to produce atransgenic hybrid plant. As used herein, “crossing” can refer to asimple X by Y cross, or the process of backcrossing, depending on thecontext.

The development of a hybrid in a plant breeding program involves threesteps: (1) the selection of plants from various germplasm pools forinitial breeding crosses; (2) the selfing of the selected plants fromthe breeding crosses for several generations to produce a series ofinbred lines, which, while different from each other, breed true and arehighly uniform; and (3) crossing the selected inbred lines withdifferent inbred lines to produce the hybrids. During the inbreedingprocess, the vigor of the lines decreases. Vigor is restored when twodifferent inbred lines are crossed to produce the hybrid. An importantconsequence of the homozygosity and homogeneity of the inbred lines isthat the hybrid created by crossing a defined pair of inbreds willalways be the same. Once the inbreds that give a superior hybrid havebeen identified, the hybrid seed can be reproduced indefinitely as longas the homogeneity of the inbred parents is maintained.

Transgenic plants of the present invention may be used to produce, e.g.,a single cross hybrid, a three-way hybrid or a double cross hybrid. Asingle cross hybrid is produced when two inbred lines are crossed toproduce the F1 progeny. A double cross hybrid is produced from fourinbred lines crossed in pairs (A×B and C×D) and then the two F1 hybridsare crossed again (A×B)×(C×D). A three-way cross hybrid is produced fromthree inbred lines where two of the inbred lines are crossed (A×B) andthen the resulting F1 hybrid is crossed with the third inbred (A×B)×C.Much of the hybrid vigor and uniformity exhibited by F1 hybrids is lostin the next generation (F2). Consequently, seed produced by hybrids isconsumed rather than planted.

All publications and patent applications mentioned in the specificationare indicative of the level of those skilled in the art to which thisinvention pertains. All publications and patent applications are hereinincorporated by reference to the same extent as if each individualpublication or patent application was specifically and individuallyindicated to be incorporated by reference.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it will be obvious that certain changes and modificationsmay be practiced within the scope of the appended claims. Thus, manymodifications and other embodiments of the invention will come to mindto one skilled in the art to which this invention pertains having thebenefit of the teachings presented in the foregoing descriptions and theassociated drawings. Therefore, it is to be understood that theinvention is not to be limited to the specific embodiments disclosed andthat modifications and other embodiments are intended to be includedwithin the scope of the appended claims.

The following examples are offered by way of illustration and not by wayof limitation.

Example 1 P14 Characterization of Drought Tolerance in the RiceG-Protein α Subunit Mutant, d1

The rice dwarf mutant, d1, contains a non-functional RGA1 gene, encodingthe GTP-binding α-subunit of the heterotrimeric G protein. This mutantwas originally isolated as a spontaneous mutant with reduced height andshorter, erect, thicker, broad, dark green leaves, compact panicles, andshort, round grains. We have examined the physiological responses of thed1 mutant to mild and severe water limitation during both vegetative andreproductive development in comparison with its background line. The d1plants present higher photosynthetic rates, stomatal conductance, andψ_(leaf) than wild type during both mild and severe water limitation,and have a greater number and percentage of tillers producing panicles,with resulting higher reproductive yield. The d1 plants also performbetter than wild-type plants under high planting densities.

FIG. 1 shows water stress during flowering and grain filling; mutantplants remain dark green and healthy while wild-type plants dry out andhave a few living leaves under severe drought. The three wateringconditions were: well-watered (100% soil relative water content),medium-water (45% soil relative water content), and low water (30% soilrelative water content) conditions. Photographs were taken 140-160 daysafter emergence.

FIG. 2 shows that d1 plants exhibit lower leaf temperatures thanwild-type plants under all 3 watering conditions. Leaf temperatures onplants 165 days after emergence were measured by infrared thermographyusing a FLIR T620 Thermal Imaging Camera (FLIR Systems, USA). In orderto obtain reliable comparisons, images were obtained over the shortesttime interval possible; approximately 15 minutes total. Pseudo-coloredtemperature scales are indicated directly on the photographs.

FIG. 3 shows that net photosynthesis and stomatal conductance arereduced more severely in wild-type plants than in d1 mutants undermedium-water (45% soil relative water content) and low-water (30% soilrelative water content) conditions, while these parameters arestatistically identical under well-watered (100% soil relative watercontent) conditions. Parameters were measured on leaves between 120 and130 days after emergence, using a Li-Cor 6400 Portable PhotosynthesisSystem. Light intensity was 500 m⁻²s⁻¹.

FIG. 4 shows that d1 mutants have higher stomatal conductance butnevertheless lose less water (have lower transpiration rates) thanwild-type plants. This is presumably due to the lower leaf temperaturesof d1 plants as compared to wild-type (as shown in FIG. 3); lower leaftemperatures result in a reduced vapor pressure deficit, i.e. a reducedphysical driving force for evaporative water loss. Measurements weremade under ambient conditions of 500 μmol m⁻²s⁻¹ light and 30° C.temperature using a Li-Cor 6400 Portable Photosynthesis System.Measurements were taken on seedlings at 40 days after emergence. Eachdata point represents an individual plant. Lines depicted are regressionlines for each genotype; ANCOVA analysis demonstrated significantdifferences (P<0.05) in the slopes.

FIG. 5 shows that the water potential (ψ_(leaf)) of d1 plants is higherthan that of wild-type plants under medium-water and low-waterconditions, and equal to that of wild-type plants under well-wateredconditions (the three watering regimes were specified above). ψ_(leaf)measurements, made using a Scholander pressure chamber, were taken fromthe flag leaf of the primary tiller of plants 120-130 days afteremergence.

Taken together, FIGS. 3-5 show that d1 plants have improved water statusand higher photosynthetic rates than wild-type plants under droughtconditions.

FIG. 6 is a graph showing the percentage of stalks flowering at the endof the reproductive phase in high water, low water and medium waterconditions. One can see that water limitation decreases the number ofstalks developing a flower head in wild-type plants but not in d1mutants.

FIG. 7 shows the average number of panicles produced through time in d1and wild-type plants. Panicle production is greater in the d1 mutantthan in wild-type plants. Water-limited conditions result in apronounced reduction in the average number of panicles produced bywild-type plants but do not affect average panicle production in d1plants.

FIG. 8 shows drought-induced grain abortion per panicle in wild-type andd1 plants under the three watering regimes. The data are from 6 paniclesrandomly selected for analysis from 6 different plants of each genotypeand water treatment combination, measured at the end of the life cycle.

Taken together, the above 8 figures show the basis for the increasedgrain yield by d1 plants as compared to wild-type plants under droughtconditions: FIG. 9 shows that estimated grain yield per plant isstatistically equal in wild-type and mutant d1 plants under well-wateredconditions and is much higher in d1 mutants than in wild-type plantsunder drought conditions.

FIG. 10 shows that in the absence of drought stress, increased plantingdensity reduces photosynthesis at light saturation to a greater extentin wild-type than in the d1 mutant. Plants were grown in monospecificstands at the indicated planting densities. Net photosynthesis at 1500μmol m⁻²s⁻¹ light was measured on the flag leaf of the primary tiller at60 days after emergence using a Li-Cor 6400 Portable PhotosynthesisSystem.

FIG. 11, from the same experiment as FIG. 10, shows that high plantingdensity compromises plant growth and survival (as indicated by plantheight) earlier in wild-type than in d1 plants.

Higher photosynthetic rates and improved survival at increased plantingdensity are favorable agronomic traits. FIGS. 10 and 11 show that thesetraits are exhibited to a greater extent by the d1 mutant than bywild-type plants.

Example 2 Plant Heterotrimeric G Protein Function: Insights fromArabidopsis and Rice Mutants Laetitia Perfus-Barbeoch, Alan M. Jones andSarah M. Assmann

Heterotrimeric G proteins have been implicated in a wide range of plantprocesses. These include responses to hormones, drought, and pathogens,and developmental events such as lateral root formation, hypocotylelongation, hook opening, leaf expansion, and silique development.Results and concepts emerging from recent phenotypic analyses ofG-protein component mutants in Arabidopsis and rice are adding to ourunderstanding of G-protein mechanisms and functions in higher plants.

Introduction

Heterotrimeric GTP-binding proteins (G proteins) provide a key mechanismby which a specific signaling cascade is switched on or off to translatean incoming signal into a specific cellular response. In recent years,much has been learned about the diversity of signal transduction throughplant G proteins thanks to the identification and mutation of genes inArabidopsis and rice (Oryza sativa) that encode specific G-proteincomponents. These components include the α, β, and γ subunits of the Gprotein heterotrimer, possible heptahelical G-protein-coupled receptors(GPCRs), and regulator of G-protein signaling proteins (RGS). Suchstudies are revealing two crucial concepts. First, some physiologicalresponses are predominantly mediated by Gα, whereas others arepredominantly mediated by Gβγ. Second, the particular role of any givenG-protein component in plant developmental processes [1,2,3^(••)] andresponses to biotic and abiotic stresses [4-7,8^(••)] can differ in acell-type- or developmental-stage-specific manner. Thus, one mutant caneven show opposite phenotypic responses to the same stimulus, dependingon the particular cell or tissue under study. To highlight theseconcepts, in this review, we discuss the latest genetic studies on plantG-protein signaling from an ‘organ’ point-of-view (FIG. 1). The readermay also be interested in reviews on plant heterotrimeric G proteinsthat have emphasized comparisons with mammalian systems [9-13].

The Heterotrimeric G-Protein Paradigm

The G protein itself consists of three different subunits, α, β, and γ(respectively named Gα, G β, and Gγ), which form a heterotrimericcomplex in the inactive state. Binding of an agonist (i.e. an activatingligand) to its specific GPCR leads to the conversion of an inactive Gprotein to its active conformation. The GPCR acts as a guaninenucleotide exchange factor, causing Gα to exchange GDP for GTP. As aresult, Gα-GTP separates from the Gβγ dimer and both Gα-GTP and the Gβγdimer separate from the receptor and can activate downstream effectors.Subsequent to signal propagation, the GTP that is bound to Gα ishydrolyzed to GDP, thereby inactivating Gα and allowing itsre-association with the Gβγ dimer to reform the inactive heterotrimericcomplex. RGS proteins act as GTPase-activating proteins (GAPs) for Gα,typically attenuating signaling by hastening the return of the G proteinto the resting state.

G-Protein Components in Arabidopsis and Rice

Candidate genes that encode polypeptides that are similar to mammalianG-protein components have been isolated from several higher plantspecies (summarized in [11]). In Arabidopsis and rice, Gα is encoded bya single copy gene, designated GPA1 or RGA1, respectively [14,15]. Gβ islikewise encoded by a single-copy gene, designated AGB1 or RGB1,respectively [16,17]. Two Gγ genes were recently isolated fromArabidopsis and rice: AGG1 or RGG1 [18,19] and AGG2 or RGG2 [19,20]. Noplant gene has been found that is highly homologous to metazoan GPCRs.However, in Arabidopsis, GCR1 is a likely candidate as a GPCR-encodinggene because it encodes a protein that has some GPCR sequence similarityand a predicted heptahelical structure that is the hallmark of bona fideGPCRs [8,21,22]. Finally, it appears that the Arabidopsis genomecontains only one member of the RGS family, RGS1 [23]. Transgenic plantsthat ectopically and/or conditionally express each of theabove-described components, except the Gγ subunit genes, have beendescribed recently (Table 1), and various single, double, and triplemutants have been generated (Table 1).

On the basis of both modeling [3^(•)] and experimentation, the basicparadigm of mammalian G-protein signaling described above also appearsto operate in plants [13]. Gα, Gβ, Gγ, GCR1 and RGS1 can all be found atthe plasma membrane of plant cells [1,8,19,22,23,24,25]. In yeasttwo-hybrid assays and co-immunoprecipitation experiments, Gβ interactstightly with both Gγ subunits in both Arabidopsis and rice [18,19,20].In rice, gel-filtration experiments have confirmed that Gβγ dimersassociate with Gα. This association is disrupted by a non-hydrolysableform of GTP, GTPγS, which is expected to maintain the activatedconformation of Gα [19]. Pandey and Assmann [8] used in planta and invitro co-immunoprecipitation as well as split-ubiquitin yeast two-hybridassays to provide the first conclusive evidence that the putative GPCR,GCR1, physically interacts with Gα. RGS1 interacts with both aconstitutively active GPA1 (GPA1^(QL), the GTPase-deficient version ofGPA1) and wild-type GPA1, and the carboxy-terminal domain of AtRGS1 hasbeen shown to exert GAP activity on a yeast Gα [23].

Striking differences also exist, however, between the G-proteincomponents of plants and those of other eukaryotic organisms: thesequence similarity of the relevant genes and proteins is limited, and amuch smaller number of genes encode each of the different components inplants than in other eukaryotes [13].

G-Protein Signaling in Seeds

Seed germination is a complex phenomenon that is modulated by numeroussignals, including gibberellins (GA), abscisic acid (ABA),brassinosteroids (BR), ethylene, light, and sugars, some acting inconcert and others in opposition [26]. Current models of seedgermination in non-graminaceous species suggest that BR act downstreamof GA to promote germination. Both ABA and sugars inhibit germination,and ethylene negatively regulates ABA's effects.

In the absence of stratification, gpa1-1 and gpa1-2 mutant seeds exhibitdelayed germination [27], suggesting that they are more dormant thanwild-type seeds. Consistent with this phenomenon, gpa1 mutants exhibitmoderately increased sensitivity to the inhibition of germination by ABAand sugars [2,27]. Many of these phenotypes are also observed inArabidopsis T-DNA insertional mutants of Pirin1, a cupin-domain proteinthat has been identified as a GPA1 interactor in yeast two-hybrid assays[27].

Because gpa1 seeds have wild-type ABA concentrations [2], the resultsdescribed above presumably reflect either an increased sensitivity toABA or a decreased sensitivity to stimulatory signals such as GA. Insupport of the latter hypothesis, the germination of gpa1 and agb1 seedsis significantly less sensitive to exogenous GA and significantly moresensitive to the GA-synthesis inhibitor paclobutrazol than thegermination of wild-type seeds [2,22]. Ullah et al. [2] speculate thatGPA1 controls the sensitivity of the GA pathway because although theoverexpression of GPA1 in Arabidopsis confers a millionfold increase inthe GA sensitivity of seed germination, the requirement for GA is notabolished. If GPA1 directly coupled the GA response, then the ectopicexpression of GPA1 would be expected to confer GA independence, which isnot the case. Ullah et al. [2] further suggest that BR controls GAsensitivity in a GPA1-dependent manner, because brassinolide (BL) rescueof germination in seeds treated with paclobutrazol is complete forwild-type seeds but only partial for gpa1 and agb1 seeds [2,22,28].

Like gpa1 mutants, gcr1 mutants exhibit reduced sensitivity toward GAand BR in seed germination, whereas GCR1 overexpression reduces seeddormancy [22,29]. Under some but not all conditions, seeds of gcr1 gpa1and gcr1 agb1 double mutants have additive or synergistic germinationresponses to GA and BR, which is unexpected if GCR1 were to functionupstream of the G protein. Thus, under some conditions, GCR1 appearsable to act independently of the heterotrimer in regulating seedgermination [22].

Seeds of the rice dwarf1 (d1) mutant, a null mutant [19′] of the rice Gαsubunit, RGA1, exhibit a morphological phenotype consisting of short,round grains [30,31]. Observations in rice are also consistent with arole for G proteins in GA-based signaling pathways and the control oftranscription in the seed. d1 mutants exhibit reduced GA induction ofa-amylase gene expression and enzyme activity in their aleurone cellsand reduced expression of the GA-induced genes OsGAMYB and GACa²⁺ ATPase[32]. Gα may also be a component of BR signaling in rice becauseBL-stimulated expression of a novel BL-enhanced gene is weaker in d1mutants than in wild-type seedlings [33]. Ueguchi-Tanaka et al. [32]suggest that there may be two separate GA-signaling pathways in rice,with either high or low sensitivity to GA, and that RGA1 may mediate theformer pathway. Both this model and the ‘GPA1 modulation’ modeldescribed above [2,32] are consistent with the current data from bothArabidopsis and rice. Hence, additional experimentation, includingdetermination of the ABA sensitivity of d1 seeds, will be required todistinguish between these two possibilities.

G-Protein Signaling in Roots

Root growth and architecture involves a balance between cell productionin the apical and lateral root meristems and the subsequent elongationof those cells. One advantage of the root as a model system fordevelopment is that it is possible to measure rates of cell productionand elongation as well as the number of lateral root primordial quiteprecisely, thereby making it possible to quantify exactly what haschanged in the roots of loss- and gain-of function G-protein mutants.The formation of lateral root meristems originates from a set of foundercells that differs from that used to form the primary meristem [34,35].Therefore, it would not be surprising if the molecular mechanisms thatunderlie the initiation of lateral and primary root meristems weredifferent. Studies on root meristem formation and maintenance usingG-protein mutants are beginning to reveal these mechanistic differences.

Primary Root

The primary root growth of wild-type plants and that of gpa1 and gcr1single mutant seedlings appears to be identical in the absence ofexogenous hormone treatment [3^(••),8^(••)]. By contrast, rgs1 mutantshave longer primary roots because of their increased cell productionrate in the primary root meristem [23^(••)]. rgs1 cells, which lack GAPactivity, are predicted to have a greater steady-state pool of activatedGα. This prediction is consistent with the observation that theexpression of a transgene that encodes GPA1^(QL) also causes acceleratedcell production by the primary root meristem [23^(••)]. This suggeststhat Gα plays a role in modulating cell division in the primary rootmeristem. The lack of a large effect of the gpa1 null mutation onprimary root growth suggests that the type of modulation that GPA1exerts may be an increase over a basal state, a state that does notrequire Ga.

In response to exogenous treatment with plant growth regulators such asABA and auxin, primary root elongation is retarded and/or the directionof primary root growth changes. The primary root elongation of gpa1,agb1, or gcr1 single mutants, as well as of double and triplecombinations of these mutants, is more sensitive to inhibition by ABAthan that of wild-type plants ([8^(••)]; S Pandey, S M Assmann,unpublished). However, the auxin inhibition of primary root length ingpa1 and agb1 mutants is the same as that in wild-type plants [3^(••)],indicating that the dependency of growth inhibition on G proteinsdiffers depending on the hormonal stimulus.

Lateral and Adventitious Roots

While the growth of the primary root of gpa1 mutants is like that ofwild-type plants under many conditions, the number of lateral roots isgreatly increased in agb1 mutants and is decreased in gpa1 mutants[3^(••)]. Opposite to its inhibitory effect on the primary root, auxinis a key activator of lateral root initiation [36]. In the presence ofauxin, agb1 plants form more lateral roots, whereas gpa1 plants formfewer lateral roots, compared to wild-type plants [3^(••)]. As isexpected if the auxin-induced phenotype for the proliferation of lateralroots is AGB1-dependent, ectopic expression of GPA1 (which is expectedto sequester AGB1 into the heterotrimeric complex) also yields anagb1-like phenotype. The expression of GPA1^(QL) has no effect on thisphenotype, a finding that is inconsistent with GPA1 acting as a positivemodulator of cell division in the lateral root meristem. Thus, Ullah etal. [3^(••)] propose that free Gβγ directly attenuates auxin-inducedcell division in lateral roots, as opposed to Gα acting to stimulatethis process.

G-Protein Signaling in Shoots

As for seed germination and root development, several differences havebeen observed between G-protein-component mutants and wild-type plantsduring the development of above-ground organs in seedlings and matureplants [10-12].

When grown in darkness, gpa1 and agb1 seedlings have shorter hypocotylsthan wild-type plants because of a reduction in cell number, and theseseedlings exhibit partially opened hooks [1,3^(••),37]. These phenotypeswere also observed in gcr1 gpa1 double, agb1 gcr1 double, and agb1 gpa1gcr1 triple mutants [22]. By contrast, rgs1 mutant seedlings have alonger etiolated hypocotyl as a result of increased cell elongation.This mutant phenotype is similar to that observed in plants that expressGPA1^(QL), consistent with the premise that, in plants as in animals,RGS proteins oppose Gα activation [22].

When grown in light, gpa1 and agb1 mutants have rounded rosette leaves[1]. The round-leaf phenotype is also found in Arabidopsis gcr1 gpa1 andagb1 gcr1 double mutants and agb1 gcr1 gpa1 triple mutants [22]. Becausegcr1 single mutants have wild-type phenotypes for both hypocotyl androsette-leaf development, GCR1 may not act as the GPCR that isresponsible for control of these developmental pathways [22].

The rice Gα (d1) mutants also exhibit an altered shoot morphology,consisting of broad, dark green leaves and compact panicles[5,30,31,32,38]. One notable contrast between Arabidopsis and rice Gαmutants, however, is that the rice mutants are dwarf but the Arabidopsismutants are not. Dwarf phenotypes are often associated with GAinsensitivity, and GA induction of internode elongation is significantlyreduced in the d1 mutants [31]. However, the GA responsiveness of theelongation of the second leaf sheath is similar in d1 mutants andwild-type plants [32]. This selective impairment of GA signaling in d1mutants suggests cell specificity in GA response, with some pathwaysbeing only marginally dependent on Ga.

During the reproductive phase of plant development, agb1-1 mutants havea floral phenotype consisting of shorter flowers and thicker siliques,but this phenotype is not shared by gpa1 mutants [1,3^(••),39].Constitutive overexpression of GPA1 reduces silique length, producing aphenotype that is similar to that of agb1. This evidence is consistentwith the idea that silique length is controlled by released Gbg[3^(••)]. gpa1 sepals and pedicels are longer, whereas agb1 sepals areshorter, than those of wild-type plants [3^(••)], findings that areagain consistent with a Gβγ-dependent pathway. Transformants thatoverexpress GCR1 flower earlier [29], but gcr1 null mutants typically donot flower later, than wild-type plants [22].

Stress Responses

G proteins are implicated in several stress-signaling pathways inplants. In mature leaves, G proteins transmit signals to molecules,including small GTPases, ion channels, and phospholipases, that areeffectors in the responses to various biotic and abiotic stressconditions, including pathogen elicitation, ozone treatment and waterdeficit.

There are no reports as yet on pathogen signaling in ArabidopsisG-protein mutants, but some defense signaling pathways in rice appear torely on RGA1. Upon infection with a virulent strain of bacterial blight(Xanthomonas oryzae pv. Oryzae [Xoo]), symptom development in d1 mutantsis more severe than that in wild-type plants [7]. By contrast, infectionwith virulent strains of rice blast fungus (Magnaporthe grisea) producesidentical lesions in d1 mutants and wild-type plants. d1 mutants exhibita highly reduced response, however, upon inoculation with avirulent riceblast [5,7]. Expression of a constitutively active OsRac1 in d1 mutantsrestores defense signaling and resistance, suggesting that RGA1functions upstream of this small GTPase [5]. Yet, in a d1 mutant cellline treated with the oligosaccharide elicitor chitin, the elicitationof defense responses such as extracellular alkalinization, generation ofreactive oxygen species, phytoalexin accumulation and the induction ofspecific genes does not differ from that of wild-type cells [40,41].Taken together, these studies indicate that the extent of G-proteincoupling of responses to both avirulent and virulent pathogens ispathogen- and elicitor-specific.

Like pathogen infection, exposure to high ozone (O₃) levels results infoliar lesions, and O₃ responses share signaling pathways and geneexpression patterns with the hypersensitive response [42]. gpa1 nullmutants and the double mutant gpa1-4 agb1-2 respond differently to O₃compared to wild-type plants, and to gcr1 and rgs1 single mutants. Themajor difference observed among these mutant genotypes is anO₃-resistant phenotype of the gpa1 lines, indicated by lack of leafcurling in response to O₃ [6].

One of the phenomena commonly observed following O₃ exposure is areduction in stomatal apertures [43], a response that is also evoked byABA. gpa1 mutants exhibit reduced O₃ sensitivity at the whole-leaflevel. At the single (guard)-cell level, gpa1 mutants also exhibitaspects of ABA insensitivity, including reduced ABA inhibition of guardcell inward K⁺ channels and altered ABA-promotion of slow anion currents[4]. Recently, the lipid metabolite, sphingosine-1-phosphate (SIP), hasbeen described as a secondary messenger for ABA responses [44,45^(••)].The guard cells of gpa1 mutants show insensitivity to inhibition ofstomatal opening by either ABA or SIP. However, ABA still induceswild-type levels of stomatal closure in gpa1 [4], whereas stomatalclosure in this genotype is insensitive to SIP. This difference impliesthat the SW response is obligatorily mediated by GPA1, whereas there isa parallel or backup pathway for ABA induction of stomatal closure thatis independent of GPA1 [45^(••)].

gcr1 mutant guard cells exhibit hypersensitivity to ABA and SP in bothinhibition of stomatal opening and promotion of stomatal closure[8^(••)], which would be unexpected if GCR1 were to transmit the ABAsignal to GPA1. Pandey and Assmann [8^(••)] therefore proposed that GCR1acts as a negative regulator of GPA1-mediated ABA responses in guardcells. Consistent with this phenomenon, gcr1 mutant plants have higherexpression levels of some known drought- and ABA-regulated genes afterexogenous ABA treatment and exhibit improved recovery following droughtstress [8^(••)].

Many enzymes, including phosphatidylinositol-phospholipase Cs (PLCs;reviewed in [46]) and phospholipase Ds (PLDs; [47,48]), act as effectorsof the ABA response during the regulation of stomatal aperture. Thesephospholipases also have been identified recently, albeit not yet inguard cells, as intracellular effectors of G protein signaling. Forinstance, using tobacco BY2 cells that overexpressed GCR1, Apone et al.[49] concluded that GCR1 regulates DNA synthesis through activation ofPLC. In Arabidopsis, PLDα1 directly binds GPA1 via a motif similar tothe DRY motif that is present in many mammalian GPCRs [50^(••)]. Bindinginhibits PLDα1 activity and is relieved upon GTP addition, suggestingthat, in vivo, G protein activation leads to the activation of PLDa1[50^(••)]. Thus, it will be of interest to assess PLC and PLD activityin guard cells in which the levels of G-protein components are altered.

Conclusions: With Few G-Protein Complexes in Plants, GPCRs and EffectorsMust Specify Signal Transduction

As is evident from the phenotypes described in this review, numerousprocesses at all stages of plant development are modulated byheterotrimeric G proteins. Many of these phenotypes appear upon nullmutation of the Gα subunit genes GPA1 or RGA1, implying dependency uponGα coupling to downstream effectors. However, some phenotypes, notablylateral root proliferation and altered silique morphology, are presentin agb1 mutants but are either absent or opposite in gpa1 mutants,implying a dependency on Gβγ-coupled signaling. But is that the wholestory? Plausibly, the different phenotypes of gpa1 and agb1 mutantscould reflect differences in the relative levels of the releasedsubunits from the heterotrimeric complex, different fluxes of signalingthrough Gα (as opposed to Gβγ) in the different cell types or organs,and/or a different relative balance in positive or negative feedback. Tosort out these issues, it will be necessary to determine the effect on agiven trait of quantitatively altered ratios of Gα to Gβγ, rather thanof the two extremes of ratios of 0 or ∞ that are created by single nullmutations. Given the plethora of G-protein-related phenotypes incombination with the dearth of heterotrimeric G-protein subunits inplant genomes, one might well predict that plants will be found to haveevolved novel and abundant mechanisms for coupling G protein componentswith downstream effector molecules.

In Arabidopsis, seeds and light-grown gpa1 seedlings show increasedsensitivities to ABA and sucrose together with decreased sensitivitiesto BL [2,27′], suggesting that identical G-protein-based signalingpathways may operate in seed germination and early seedling development.In mature rosette leaves, however, gpa1 guard cells exhibit reducedrather than enhanced sensitivity to ABA. In rice, internode sensitivityto GA is strongly reduced in d1 mutants, yet GA-regulation ofleaf-sheath elongation is scarcely affected. These differentialsensitivities indicate that the roles of GPA1 must be cell- andtissue-specific, presumably reflecting cell- and tissue-specificeffectors and/or GPCRs. Cell-specific mechanisms for G-protein-coupledsignaling have precedent in animal systems (e.g. [51]).

By parallel reasoning, one might expect a proliferation of cell-specificGPCRs in plants. However, if this is true, the plant GPCRs must bedefined by functionality rather than by sequence similarity; GCR1 is thesole candidate GPCR to be identified in Arabidopsis on the basis ofhomology criteria and its sequence similarity to known GPCRs is limited.The observations that GCR1 is not implicated in many of the pathwaysthat are affected by mutation of GPA1 and/or AGB1, and that theABA-related phenotypes of gcr1 mutants are opposite to those of gpa1mutants, further highlight our lack of knowledge about components thatfunction upstream of plant G-protein heterotrimers. Signals may betransduced either via novel GPCRs or through proteins that transmitsignals to G proteins independently of GPCRs [51,52]. Furthermore,plant-specific ‘unconventional’ G proteins, such as A. thaliana ExtraLarge G Protein1 (XLG1), a protein that has significant similarity to Gαsubunits and exhibits GTP-binding capability [11,53], could potentiallypartner with components of G-protein pathways. Thus, the future isbright for model plant systems such as Arabidopsis and rice tocontribute new insights regarding this ubiquitous eukaryotic signalingparadigm.

In Arabidopsis, GCR1 may positively regulate seed germination bycoupling BR promotion of GA-stimulated germination. GCR1 also can actindependently of GPA1 and AGB1 in a pathway to regulate GA-stimulatedgermination [23^(••)]. RGS1 antagonizes the activation of GPA1[23^(••)]. Pirin1 may positively regulate seed germination by overcomingthe negative effect of ABA or by activating germination-promotingpathways [27′]. In rice, RGA1 may work in a high-sensitivity GA pathwaythat regulates the induction of Ca²⁺-ATPase and α-amylase, leading toseed germination [32]. RGA1 may also be a component of BR signaling[33]. In addition, there may be an alternative GA pathway that alsoinduces a-amylase but does not involve RGA1 [32]. (b) Celldivision/elongation. During seedling growth, GPA1, AGB1 and GCR1 may actin the inhibition of primary root development by ABA ([8^(••)]; SPandey, S M Assmann, unpublished). Furthermore, GCR1 negativelyregulates ABA-induced gene expression [8^(••)]. AGB1 and GPA1 activatecell division in both hypocotyls and leaves [1,2,3^(••),37] whereas RGS1antagonizes the activation of GPA1 in apical root meristems [23^(••)].Auxin treatment also increases GPA1 transcript levels and decreases AGB1transcript levels (not shown in figure, [3^(••)]). During lateral rootformation, AGB1 functions downstream of GPA1 and inhibits auxin-inducedcell division, and GPA1 inhibits AGB1 function [3^(••)]. (c) Stressresponses. According to the leaf curling phenotype, GPA1 promotes the 03sensitivity of Arabidopsis plants [6]. Drought stress and ABA treatmentinhibit stomatal opening and promote stomatal closure. ABA triggers SPformation, which is coupled by GPA1 to inhibit plasma membrane inwardlyrectifying K+ channels and to activate slow anion channels, resulting inthe inhibition of stomatal opening and the promotion of stomatal closure[4,45^(••)]. The GPCR-like protein GCR1 directly binds to GPA1 andnegatively controls ABA- and S1P-regulation of stomatal apertures [8].In rice, responses to avirulent rice blast fungus, including theaccumulation of transcripts for the small GTPase, OsRac1, are attenuatedin the RGA1 mutant d1. OsRac1 acts as a key molecular switch formultiple signaling pathways, such as the production of reactive oxygenspecies that lead to disease resistance. Expression of constitutivelyactive OsRac1 in the d1 mutant restores defense signaling [5]. Inresponse to virulent strains of bacterial blight, lesions are moresevere in the d1 mutant than in wildtype plants [7]. (d) Morphology. InArabidopsis, both GPA1 and AGB1 modulate leaf development and shape[1,39]. gpa1 and agb1 mutants exhibit rounded lamina. AGB1 is alsoinvolved in flower and fruit development [1,3^(••),39]. In agb1, thefloral buds at the inflorescence apex are more tightly clustered, thesiliques are shorter, and the silique tips are more blunt than those ofwildtype plants. In rice, RGA1 modulates plant stature by regulatinginternode and panicle elongation, and also influences the color of leafblades and sheaths and grain shape [32].

TABLE 1 Mutant and transgenic lines for Gα, Gβ, GCR1 and RGS 1Name/Allele Ecotype/cultivar cDNA Status of transcript/translationproduct Phenotype comparison with wild-type ecotypes Mutant loss offunction for Gα subunit in Arabidopsis (A. thaliana) Phenotypes of gpa1mutants gpa1-1 Ws T-DNA insertion in 7^(th) intron. Lacks full-lengthtranscript Less sensitive to GA and BL stimulation of germinationWisconsin KO Arabidopsis facility α population [1]. [1, 2]. Moresensitive to the GA biosynthesis inhibitor paclobutrazol [2, 22].Hypersensitive to ABA and sugar inhibition of germination [2, 27*]. Indarkness, partial deetiolation: open hook; shorter hypocotyls caused byreduced cell division [1]. gpa1-2 Ws T-DNA insertion in 8^(th) exon.Lacks full-length transcript Primary root forms fewer lateral rootprimordia [1]. Wisconsin KO Arabidopsis facility [1]. Less sensitive toauxin promotion of laterial root formation α population. [3**]. Roundedlamina shape [1, 37]. Leaf cells are fewer and larger [1]. Longer sepalsand pedicels [1]. Less sensitive to O3 [6]. gpa1-3 Col-0 T-DNA insertionin 9^(th) exon. Lacks full-length transcript More water loss [4]. Salkcollection. [37]. Insensitive to ABA inhibition of stomatal opening [4].Insensitive to ABA inhibition of inward K⁺ channels [4]. Insensitive toS1P promotion of stomatal closure [45**]. gpa1-4 Col-0 T-DNA insertionin 12^(th) itron. Lacks full-length transcript Altered sensitivity toABA activation of slow anion channels Salk collection [37]. [4].Insensitive to S1P activation of slow anion channles [45**]. Phenotypesof Daiokoku dwarf1 (d1) mutants (DK22, Mutant loss of function for Gαsubunit in rice (Oryza sativa) HO541, CM 1361-1, T65d1, rga1) DK 22Nipponbare Point mutation of G598 to T in 8^(th) Stop codon generatedShorter and rounded grains [30, 31]. exon. [31, 40]. Reduced GA and BLstiumlation of gene expression [32, 33]. Protein null [19*]. Ho 541Nipponbare Spontaneous mutant: Deletion of RGA1 transcript null [3-]Shorter and darker green leaves, more compact particle [5, 30-32, 833basepairs between 1^(st) exon and 38]. intron. CM 1361-1 KinmazeInsertion between nucleotides 354-355 Predicted protein lacks Shorterinternodes - may be due to a decrease in the number GTP-, effector- andof cells per internode [31]. receptor-binding regions Reduced GAstimulation of internode growth [32]. [31]. Normal GA stimulation ofsecond leaf sheath elongation [32]. T65d1 Taichung 65 Deletion ofnucleotides 1003-1004. Stop condon generated Reduced hypersensitiveresponse to infection by rice blast before third effector-binding fungus[5]. region [32]. rga1 Nipponbare Antisense suppression. RGA1 transcriptnull line Increased sensitivity to infection by virulent strain of [31]bacterial blight [7]. HO 532 HO 533 HO 537 Nipponbare Spontaneousmutants. [30] Not used for phenotypic analysis. HO 538 HO 552 FL2Nipponbare Marker line derived from HO 538. [30] Not used for phenotypicanalysis. ID 1 Shiokari Deletion of nucleotides 1003-1004. [31] Not usedfor phenotypic analysis. CM392; Kinmaze Induced by N-methyl- [5, 30] Notused for phenotypic analysis. 1729; 248; N-nitrosourea. 723; 1232 DKT 1Taichung 65 Point mutation of A1075 to T. [31] Not used for phenotypicanalysis. DK 2 Taichung 65 Deletion betwween nucleotides Predicted tolack GTP- Not used for phenotypic analysis. 932-979 binding region [31].Mutant gain of function for Gα subunit in Arabidopsis Phenotypes of GPA1overexpressors Q222L or Col 35S promoter::point mutation Mutationdisables GTPase No effect on auxin-induced cell divison in lateral roots[3**]. GPA1* A1264 to T derived from GPA1 activity, leading to No auxineffect on hypocotyl length [3**]. cDNA. constitutively active Gα [1,3**, 37]. GPA1^(α) Ws 35S promoter::constitutive form of Overexpressionof Increased hypocotyl length caused by increased cell GPA1 cDNAconstitutively active Gα elongation [23**]. (GPA1^(QL)) [23**]. Longerprimary roots caused by increased cell production [23**]. cGα Ws DEXinducible Overexpression of Under low light condition, shorterhypocotyls are caused by a promoter::constitutive form of constitutivelyactive Gα reduction of cell elongation, also smaller cotyledons and GPA1cDNA. (GPA1^(QL)) [54]. increased stomatal density in hypocotyl [54].wGα Ws DEX inducible promoter:: Overexpression of full- Under low lightcondition, shorter hypocotyls are caused by a GPA1 cDNA. length GPA1protein [54]. reduction of cell elongation, also smaller cotyledons andincreased stomatal density in hypocotyl [54]. gpa1 Col-0 DEX induciblepromoter:: Complementation in gpa1 Hypersensitive to GA stimulation ofgermination [2]. (GPA1) GPA1 cDNA. background [3**, 37]. In darkness,shorter hypocotyls [37]. Hypocotyl hypersensitive to auxin-inducedadventitious root formation [3**]. 35S::GPA1- Col 35S promoter::GPA1cDNA fused Overexpression of GFP with GFP. fluorescent GPA1 [23**]. GOXCol DEX inducible promoter: Overexpression of GPA1 Mimics agb1-2 lateralroot phenotype: more lateral roots GPA1 cDNA: [2, 37]. [3**]. GOX1Tobacco cells DEX inducible promoter:: Transformed BY2 cells Shortercell cycle [1]. Nicotiana GPA1 cDNA. overexpressing GPA1 HigherPtdlns-PLC activity [49]. tabaccum cv. [1, 49]. Higher Ins(1, 4, 5)P₃content [49]. BY2 Mutant gain of function for Gα subunit in ricePhenotypes of RGA1 overexpressors QL/d1 or Nipponbare 35S promoter::point mutation Expression of constitutively Active form GTP-Gα presentsfee from Gβ or Gγ subunits Q223L Q223 to L derived from RGA 1 active Gαin d1 background [9*]. cDNA. [19*]. Mutant loss of function for Gβsubunit in Arabidopsis Phenotypes of agb1 mutants agb1-1 or Col Ethylmethanesulfonic acid Mutant transcript slightly Less sensitive to GA andBR stimulation of germination [22]. elk4 mutagerized. Missense mutation:larger because of splicing More sensitive to the GA biosynthesisinhibitor paclobutrazol failure to splice out the 1^(st) intron.failure. Stop condon [2, 22]. Hypersensitive to sugar inhibition ofgermination [2]. generated [39]. In darkness, partial de-etiolation:open hook; shorter hypocotyls caused by reduced cell division [1].Hypocotyl hypersensitive to auxin-induced adventitious root formation[3**]. Primary root forms more lateral root primordia [3**]. agb1-2Col-0 T-DNA insertion in 4^(th) exon. Lacks full-length transcript Moresensitive to auxin promotoino of lateral root formation Salk collection.[3**]. [3**]. Rounded lamina shape and presence of islands of smallcells that create a crinkly surface [3**. 39]. Shorter flowers andsepals [39]. Shorter and thicker siliques [39]. Mutant gain of functionfor Gβ subunit in Arabidopsis Phenotypes of AGB1 agb1-1 ColTransformation with genomic Complementation in agb1-1 (AGB1) fragmentcontaining AGB1 gene background [39]. and promoter. agb1-1 Col-0 DEXinducible promoter:: Complementation in agb1-2 Decreased auxin-inducedlateral root formation relative to (AGB1) AGB1 cDNA. background [3**].agb1 [3**]. BOX Col-0 DEX inducible promoter:: Overexpression of AGB1AGB1 cDNA. [3**, 37]. Mutant loss of function for GCR 1 in ArabidopsisPhenotypes of gcrf mutants gcr1-1 Col-0 T-DNA insertion in 8^(th)intron. Lacks full-length transcript Less sensitive to GA and BRstimulation of germination [22]. Salk collection. [22]. Hypersensitiveto ABA inhibition of germination [8**]. gcr1-2 Col-0 T-DNA insertion in6^(th) exon. Lacks full-length transcript Hypersensitive to the GAinhibitor paclobutrazol [22]. Salk collection. [22]. Increased ABApromotion of ABA-regulated gene expression [8**]. gcr1-3 Ws T-DNAinsertion in 2^(nd) intron. Lacks full-length Increased resistance todrought stress [8**]. Wisconsin Arabidopsis KO transcript[8**].Hypersensitive to ABA and S1P inhibition of stomatal facility BASTApopulation. opening [8**]. gcr1-4 Col T-DNA insertion in 3^(rd) intron.Lacks full-length transcript Hypersensitive to ABA and S1P promotion ofstomatal SAIL collection of TMRI. [8**]. closure [8**]. Flowers slightlyearlier [22]. Mutant gain of function for GCR1 in Arabidopsis Phenotypesof GCR1 overexpressors gcr1-3 Ws DEX inducible promoter::GCR1 Expressionin gcr1-3 GCR1-FLAG immunoprecipitates with GPA1 [8**]. (GCR1) cDNAfused with FLAG tag. background [8**]. 35S::GCR1- Col 35S promoter::GCR1Overexpression of GFP cDNA fused with GFP. fluorescent GCR1 [22]GCR1-over- Col 35S promoter::GCR1 Overexpression of GCR1 Lacks seeddomancy [29]. expressing cDNA [29]. Increawsed expression of germinationassociated genes [29]. lines Early flowering [29] GCR1-over- Tobaccocells 5S promoter::GCR1 Transformed BY2 cells Increased DNA synthesis[29]. expressing Nicotiana cDNA overexpressing GCR1 Higher PtdIns-PLCactivity [49]. BY2 cells tabaccum cv. [29, 49]. Higher Ins(1, 3, 5)P₃content [49]. BY2. Mutant loss of function for RGS1 in ArabidopsisPhenotypes of rgs1 mutants rgs1-1 Col-0 T-DNA insertion in 6^(th)intron. Lacks full-length transcript Mimics GPA1^(QL) phenotype underdarkness: longer Salk collection. [23**]. hypocotyls caused by increasedcell elongation [23**]. Longer primary roots caused by increased cellproduction in light [23**]. rgs1-2 Col-0 T-DNA insertion in 9^(th)intron. Lacks full-length transcript Insensitive to 6% D-glucoseinhibition of seedling growth Salk collection. [23**]. [23**]. Mutantgain of function for RGS1 in Arabidopsis Phenotypes of RGS1overexpressors 35S::RGS1- Col 5S promoter::RGS1 Overexpression of GFPcDNA fused with GFP fluorescent RGS1 [23**]. ROX Col-0 DEX induciblepromoter:: Overexpression of full Mimics gpa1 mutant hypocotyl phenotypeunder darkness: RGS1 open reading frame length RGS1 protein [23**].shorter hypocotyl [23**]. Hypersensitive to 6% D-glucose inhibition ofseedling growth [23**]. Loss of function double/triple mutants inArabidopsis Phenotypes double/triple mutants gpa1-4 Col-0 Cross betweengpa1-4 and agb1-2. [37] Less sensitive to GA and BR stimulation ofgermination agb1-2 (same sensitivity as agb1 mutant [22]). Shorterhypocotyls and partially opened hooks [37]. Rounded lamina shape [22].Less sensitive to O₃ [6]. gcr1-2 Col-0 Cross between gcr1-2 and gpa1-4[22, 37] Less sensitive to GA and BR stimulation of germination gpa1-4agb1-2. (additive or synergistic effect of mutations [22]).gpa1phenotype under darkness: shorter hypocotyl and partially openedhook [22]. gpa1 leaf morphology: rounded lamina shape [22]. Lesssensitive to GA and BR stimulation of germination (additive orsynergistic effect of mutations [22]. agb1-2 Col-0 Cross between gpa1-4agb1-2 and [22] agb1 phenotype under darkness: shorter hypocotyl andgcr1-2 gcr1-2. partially opened hooks [22]. agb1 leaf morphology:rounded lamina shape [22]. agb1-2 Col-0 Cross between gpa1-4 [22] Lesssensitive to GA and BR stimulation of germination gcr1-2 agb1-2 andgcr1-2. (additive or synergistic effect of mutations [22]). gpa1-4 gpa1and agb1 phenotype under darkness: shorter hypocotyl and partiallyopened hooks [22]. gpa1 and agb1 phenotype under darkness: shorterhypocotyl and partially opened hooks [22]. gpa1 and agb1 leafmorphology: rounded lamina shape [22]. agb1-1 Col Cross between agb1-1and [39] Shorter petiole, shorter lamina than either agb1 or er105er-105 receptor-like kinase erecta mutant, single mutant, suggestingthat ER and AGB1 function in er-105 parallel pathways controlling thesecharacteristics [39]. D1 slr Nipponbare Cross between d1 and GA [32] SLRis epistatic to D1 supporting RGA1 involvement in GA insensitive mutantslr. signaling [32]. 35S, cauliflower mosaic virus 35S promoter; BOX,AGB1 overexpressing lines; Col, Columbia; DEX, dexamethansone; elk4,erecta like 4 mutant; er-105, receptor-like kinase erecta mutant; GFP,green fluorescent protein; GOX, GPA1 overexpressing lines; Ins(1,4,5)P₃,inositol-1,4,5-trisphosphate; PtdIns-PLC,phosphatidylinositol-phospholipase C; ROX, RGS1 overexpressing lines;SAIL, Syngenta Arabidopsis Insertion Library; slr, slender rice mutant;TMRI, Torrey Mesa Research Institute; Ws, Wassilewskija.

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Example 3 Heterotrimeric G Proteins Regulate Reproductive TraitPlasticity in Response to Water Availability Summary

Phenotypic plasticity is the ability of one genotype to displaydifferent phenotypes under different environmental conditions. Althoughvariation for phenotypic plasticity has been document in numerousspecies, little is known about the genetic mechanisms underlyingphenotypic plasticity. Given their widespread roles in hormonal andenvironmental signaling, we examined whether genes which encodeheterotrimeric G proteins are plasticity genes.

We grew multiple alleles of heterotrimeric G-protein mutants, togetherwith wild-type Arabidopsis thaliana, under different watering regimes todetermine the contributions of G-protein genes to phenotypic plasticityfor a number of developmental and reproduction-related traits.

G-protein mutations did not affect significantly the amount ofphenotypic variation within an environment for any trait, but did affectsignificantly the amount of phenotypic plasticity for certain traits.

AGB1, which encodes the 13 subunit of the heterotrimeric G protein inArabidopsis, is a plasticity gene and regulates reproductive traitplasticity in response to water availability, resulting in increasedfitness (defined as seed production) under drought stress.

Introduction

Heterotrimeric G proteins are multisubunit guanosine triphosphate(GTP)-binding proteins that function in the transduction of externalsignals into cellular responses. Because G proteins regulate a largearray of cellular and developmental processes in both plants andanimals, it is of interest to evaluate their potential impact ondevelopmental plasticity and fitness. According to the paradigm ofG-protein signaling, the G protein is activated following the binding ofa ligand to an associated membrane-bound G-protein-coupled receptor(GPCR). This binding results in a conformational change in the alphasubunit (Gα) and the subsequent exchange of GTP for guanosinediphosphate by Gα, resulting in the dissociation of Gα from the betagamma dimer (Gβγ). Gα and/or Gβγ are then free to interact withdownstream signal effectors until the intrinsic GTPase activity of Gαresults in the reassembly of the inactive trimer (Assmann, 2002).

In mammals, there are a number of genes which encode heterotrimericG-protein subunits and hundreds of GPCRs have been predicted, resultingin a large, diverse assortment of potential G-protein signaling pathways(Fredriksson & Schioth, 2005; McCudden et al., 2005). Numerous ligandshave also been identified for mammalian GPCRs, including light, sensorymolecules including odors and tastes, hormones, neurotransmitters andbacterial toxins (Civelli, 2005), and mutations in mammalian G-proteinsubunits often result in genetic disorders (Spiegel & Weinstein, 2004;Weinstein et al., 2006).

Plants possess few genes which encode G-protein subunits, and mutationsin these genes, despite their broad expression throughout the plantbody, do not result in lethality or in extreme phenotypes under ‘ideal’laboratory growth conditions (Perfus-Barbeoch et al., 2004). TheArabidopsis thaliana genome contains single genes encoding Gα (GPA1) (Maet al., 1990) and Gb (AGB1) (Weiss et al., 1994) subunits, and two knownGγ (AGG1 and AGG2) (Mason & Botella, 2000, 2001) genes. GPCR diversityis also reduced in Arabidopsis; only one putative GPCR, GCR1, has beenfunctionally characterized (Pandey & Assmann, 2004), although severaldozen additional genes have been predicted to function as GPCRs based ontopology prediction (Moriyama et al., 2006; Gookin et al., 2008) andcoupling to GPA1 in yeast (Gookin et al., 2008). To date, somephenotypes of Arabidopsis G-protein mutants, such as leaf morphology andlateral root production (Ullah et al., 2001, 2003), have been shown tobe regulated by G-protein subunits in congruence with classicalmammalian paradigms, whereas other phenotypes, such as root waving andcontrol of floral and fruit morphology (Pandey et al., 2008; Trusov etal., 2008), suggest unique variants of plant G-protein regulatory modes(Assmann, 2005; Temple & Jones, 2007). Such variants may bemechanistically related to plant-specific aspects of the G-proteincomplement, including the slow GTPase activity of the plant Gα subunit(Johnston et al., 2007; Pandey et al., 2009), the existence of anunusual class of plant-specific Gα-like proteins, the extra-large Gproteins (Lee & Assmann, 1999; Pandey et al., 2008) and the presence inArabidopsis of novel GPCR-like regulatory proteins, the GTG and RGSproteins (Chen et al., 2003; Pandey et al., 2009).

Despite the paucity of heterotrimeric G-protein subunits in theArabidopsis genome, functional studies of G-protein mutants have showndiverse roles for heterotrimeric G proteins in germination, development,phytohormone responses [abscisic acid (ABA), auxin, brassinosteroids,gibberellins], stress responses (ozone, reactive oxygen species,pathogens) and stomatal aperture regulation (Ullah et al., 2001, 2002,2003; Wang et al., 2001, 2007; Pandey & Assmann, 2004; Joo et al., 2005;Llorente et al., 2005; Pandey et al., 2006; Fan et al., 2008; Zhang etal., 2008a; Zhang et al., 2008b). How a limited number of heterotrimericG-protein subunits can transduce such a large number of hormonal andenvironmental signals is a fundamental question in plant G-proteinsignaling (Assmann, 2004). Further characterization of GTGs and otherunconventional G proteins, such as the XLGs (Lee & Assmann, 1999; Dinget al., 2008), and the identification of GPCR ligands, potentialtissue-specific GPCRs, and G-protein signaling effectors in plants mayhelp to elucidate this question. An additional model which has beenproposed is that G proteins may serve as signal modulators instead ofdirect transducers of signals (FIG. 1). By functioning as ‘cross-talkhubs’, G proteins could fine tune a phenotype or physiological responsebased on multiple signals/environmental inputs (Assmann, 2004). Thismodel also addresses another paradox in plant G-protein signaling: why,if G proteins are important to plant physiology, are G-protein mutationsnot lethal in plants? A mutation may not be lethal if additional copiesor similar versions of the gene exist in the genome or if the expressionof the gene is specific to a certain stress (e.g. cold shock) or to aless vital plant tissue or cell type (e.g. trichomes). However, none ofthese situations applies to Arabidopsis as Gα and Gβ are both encoded bysingle, canonical genes which are widely expressed throughout the plant(Ma et al., 1990; Huang et al., 1994; Lease et al., 2001; Anderson &Botella, 2007). Alternatively, if G proteins function in directinghormonal and environmental cross-talk, they may be required only in theproduction of the ‘optimal’ phenotype, and the direct transducers of thesignal would still function in the absence of functional G-proteinsubunits.

Plants, being sessile organisms, are hypothesized to have evolvedincreased phenotypic plasticity, the ability of one genotype to displaydifferent phenotypes under different environmental conditions, comparedwith their mobile animal counterparts (Bradshaw, 1972; Schlichting,1986; Sultan, 1987; Huey et al., 2002). Heightened plasticity in plantswould allow plants to compensate for inescapable and inhospitableenvironments. Although variation for plasticity has been documented innumerous plant and animal species, and many theories have been proposedconcerning the ecological and evolutionary significance of thisvariation, very little is known about the explicit genetic machinerywhich underlies phenotypic plasticity.

The phenotypic plasticity (or lack thereof) of a trait can begraphically represented by a reaction norm, which is a plot of the meanphenotypic value of the trait in different environmental conditions(FIG. 2). A horizontal reaction norm indicates that the trait lacksplasticity, whereas a line with a nonzero slope or a curved line isindicative of phenotypic plasticity. As plasticity genes control theshape or slope of the reaction norm of a trait, when these genes aremutated, it is expected that the shape/slope of the reaction norm willdiverge from that of the wild-type. Mutations may alter the height ofthe reaction norm without affecting the overall plasticity for a trait(line C), affect the amount of plasticity for a trait (line B) or maychange the direction of plasticity for a trait (line D). Differences inreaction norm shapes (plasticities) among genotypes can be detected andtested using analysis of variance (ANOVA)-based statistical methods.Specifically, a significant genotype×environment/treatment interactionterm for a trait indicates that there is variation for plasticity amongthe genotypes, that is, the response curves have differentshapes/slopes.

Although functional analysis of specific genic mutants is a widespreadmethod to determine gene function, this technique has been applied tophenotypic plasticity studies only in a few instances, which havefocused mainly on photoreceptor genes. For example, in Arabidopsis, thisapproach has been employed to study the genetic basis of phenotypicplasticity in photomorphogenetic responses (Pigliucci & Schmitt, 1999,2004). Arabidopsis hy1 and hy2 photoreception mutants, which displayconstitutively active shade avoidance responses, showed reduced fitnessunder some environmental conditions relative to the more plasticwild-type (Pigliucci & Schmitt, 1999). This result suggests that HY1 andHY2 (which encode a plastid heme oxygenase and a phytochromobolinsynthase, respectively) (Muramoto et al., 1999; Kohchi et al., 2001) areplasticity genes. In addition, naturally occurring polymorphism of thephotochrome PHYB locus has been associated with altered light responsesin Arabidopsis; however, phenotypic plasticity was not measuredexplicitly (Filiault et al., 2008). In field experiments, plantsharboring mutations in phototropin blue light photoreceptors showedreduced fitness relative to the wild-type under a range of lightconditions; however, significant genetic variation for phenotypicplasticity was observed only for the seedling emergence rate (Galen etal., 2004).

Genetic variation for plasticity has also been documented amongwild-type accessions of Arabidopsis (Pigliucci & Kolodynska, 2002;Schmuths et al., 2006; Brock & Weinig, 2007), and naturally occurringvariation for plasticity within plant species has been assessed inquantitative trait locus (QTL)-based phenotypic plasticity studies.Using recombinant inbred lines in lieu of genetic mutants, these studieshave lent additional support for the existence of plasticity genes.Studies on recombinant inbred lines of Arabidopsis (Kliebenstein et al.,2002; Ungerer et al., 2003; Juenger et al., 2005), barley (Lacaze etal., 2009) and poplar (Wu, 1998) found significant QTL×environmentinteraction for a number of traits. Specifically with regard to droughtstress in Arabidopsis, Hausmann et al. (2005) found significantrecombinant inbred line×environment interactions for a number of wateruse traits, further supporting the existence of genes which regulatephenotypic plasticity to drought stress in Arabidopsis.

The signaling cross-talk mechanism discussed above may be an importantcomponent of phenotypic plasticity, as phenotypes could be tweaked onthe basis of multiple environmental inputs. A mutation in a G-proteinsubunit might decrease cross-talk and therefore reduce the plant'sability to adjust a phenotype or response to changing environments basedon multiple signals. Specifically, a G-protein mutation might affect thedegree of plasticity of a trait (FIG. 2, line B), the amount ofvariation within an environment for a trait (that is the ‘noisiness’ ofthe trait) or might simply shift the mean value of the trait away fromthe wild-type value (FIG. 2, line C) (Assmann, 2004). Therefore, bystudying populations of G-protein mutants under multiple environments,we might reveal whether G-protein genes are plasticity genes, as well asevaluate the importance of G proteins to plant fitness. In addition,previous studies of heterotrimeric G proteins have, to a large extent,focused on guard cell physiology (Wang et al., 2001; Pandey & Assmann,2004; Fan et al., 2008) and cell division (Ullah et al., 2001, 2003;Chen et al., 2006). By studying whole-plant phenotypic plasticityresponses of G-protein mutants, we might reveal novel functions of Gproteins that could not be identified by previous cell-centeredapproaches.

As G-protein signaling has been implicated in stomatal apertureregulation (Wang et al., 2001; Pandey & Assmann, 2004; Fan et al.,2008), stomatal density (Zhang et al., 2008a) and seed and seedling ABAresponses (Pandey et al., 2006), we chose G-protein regulation ofphenotypic plasticity and plant fitness under drought as the focus ofthe present study. The following questions were asked:

1. Do G-protein mutations alter the shape/slope of reaction norms inresponse to water availability, that is are G-protein genes ‘plasticitygenes’?

2. Does a G-protein mutation affect the level of phenotypic variationwithin an environment? 3. What are the fitness consequences of G-proteinmutations in different environments?

Using multiple alleles of gpa1, agb1 and gcr1 mutants, we foundsignificant variation for plasticity for a number ofreproduction-related traits in response to water availability. agb1mutants showed significantly reduced plasticity for inflorescenceheight, number of fruits and seed number per fruit. Interestingly, agb1mutants showed enhanced fitness under drought stress compared with thewild-type, but all G-protein mutants showed reduced fitness under amplewater conditions. These data support the hypothesis that heterotrimericG-protein genes are indeed plasticity genes in plants.

Materials and Methods

Plant Growth Conditions and Water Treatments

All Arabidopsis thaliana (L.) Heynh seeds used in this experiment werecollected from parent plants that were grown together under uniformconditions. gpa1-3, gpa1-4, agb1-1, agb1-2, gcr1-1, gcr1-2 andgpa1-4agb1-2 mutants have all been described previously and weregenerated using the ecotype Col (Lease et al., 2001; Jones et al., 2003;Ullah et al., 2003; Chen et al., 2004). All mutants are TDNA insertionalmutants, with the exception of agb1-1, which is anethylmethanesulfonate-generated point mutation (Lease et al., 2001). Ithas been determined that gpa1-3 and gpa1-4 are null mutants at both thetranscript and protein levels (Jones et al., 2003). agb1-2, gcr1-1 andgcr1-2 are all transcript null alleles (Ullah et al., 2003; Chen et al.,2004). agb1-1 produces a larger and less abundant AGB1 transcriptcompared with the wild-type as a result of a destabilizing pointmutation, which results in a failure to splice out the first intron andthe introduction of a premature stop codon (Lease et al., 2001). Allalleles were backcrossed once in our laboratory and the genotypes ofparent plants were confirmed via PCR of genomic DNA. Seed storage wasidentical for all seed lots. Cold stratified seeds (stratified at 4° C.for 48 h in darkness on wet filter paper) were sown directly on thesurface of a soil mix composed of Miracle-Gro potting mix (The ScottsCo, Marysville, Ohio, USA), Turface Greens Grade fritted clay (ProfileProducts LLC, Buffalo Grove, Ill., USA) and perlite in a 16:8:1 volumeratio. The plants were grown in Kord 90 mm press-fit pots (Kord ProductsInc. Brampton, Ontario, Canada) in a walk-in Conviron growth chamber(Conviron Inc. Winnipeg, Manitoba, Canada). The photoperiod was 12 hlight (140 μmol m⁻² s⁻¹, 21° C.) and 12 h dark (19° C.) and the relativehumidity was 60%.

Three weeks after sowing, the plants were treated with one of threewatering regimes: ample water, moderate drought or severe drought. Themoderate and severe drought designations are relative to the ample watertreatment for our experiment. Plants were individually watered using abottle-top volumetric dispenser. Plants subjected to ample watering hadcontinually moist soil (c. 95% of the soil water-carrying capacity) andweekly water applications ranging from 55 to 170 ml depending on theplant age. Ample water-treated plants never wilted between waterings,showed no signs of waterlogging and were healthy in appearance. Severedrought-treated plants had soil which dried out completely betweenwatering (c. 20% of the soil water-carrying capacity) and had weeklywater applications ranging from 10 to 50 ml. Severe drought-treatedplants displayed considerable wilting between waterings. Plantsreceiving the moderate drought treatment received approximately twicethe volume of water applied to the severe drought-treated plants (c. 40%of the soil water-carrying capacity). Moderate drought-treated plantsshowed some turgor loss between watering, but to a lesser extentcompared with the severe drought-treated plants. Water application wasadjusted for treatment and plant age, and all plants within a treatmentreceived the same amount of water. Relative water content measurementsof 5-wk-old fully expanded leaves from three blocks showed nosignificant differences between the genotypes for any watering regime,indicating that the levels of drought stress were consistent acrossgenotypes (data not shown). The average leaf relative water contents foreach treatment were 76% for ample water, 65% for moderate drought and61% for severe drought. These values are within the wide range of leafrelative water content values utilized for Arabidopsis drought stress inother published reports (Gigon et al., 2004; Rizhsky et al., 2004).

Experimental Design and Response Variables

Plants were arranged in a split-plot design. Three trays, eachrepresenting one water level, were clustered in a block, and 12 blockswere placed on separate shelves in the growth chamber. Genotypes wererandomly assigned a position within a tray with two genotype replicatesper tray. There were two replicate plants×8 genotypes×3 treatments×12blocks for a total population of 576 plants. The transition fromvegetative to reproductive growth was assessed by recording theflowering time (days from sowing), when the first open flower wasvisible, for each plant. Because of the large population size and thefact that flowering times were affected by treatment and genotype, eachplant was individually harvested 4 wks. after the plant began to flowerand the following variables were recorded: inflorescence height (cm),number of primary lateral branches and number of fruits plus any pistilwhich showed elongation or swelling. Excised rosettes were dried at 70°C. until a constant mass was achieved, and the dry mass was determined.For three blocks of plants, five fruits were harvested (two from themain inflorescence and three from the lateral branches), and the seednumber per fruit was determined using a dissecting scope. Aborted orshriveled seeds were excluded from the seeds per fruit measurements.Seed production was estimated for each plant in the three blocks whichhad seeds per fruit measurements as (total fruit number×seeds perfruit). Relative fitness (total seed number×mean total seed number forwater level) was calculated post hoc for the three blocks for whichtotal seed production was determined.

Statistical Analysis

Experiment-wide variances for genotype means under ample water anddrought stress were calculated using Minitab 15 (Minitab Inc. StateCollege, Pa., USA). F test equal variance tests were performed inMinitab between mutant and wild-type trait variances from ample waterand severe drought stress treatments. Eighty-four F tests were performedand the sequential Bonferroni correction was applied to keep atable-wide a of 0.05 (Rice, 1989).

Multivariate and univariate analyses were performed using Proc GLM inSAS 9.1 (SAS Inc. Cary, N.C., USA). As plant mortality resulted in anunbalanced design, the two genotype×treatment replicates within a blockwere averaged to enable analysis by Proc GLM. Multivariate analysis ofvariance (MANOVA) was first performed to identify whether there weresignificant effects of genotype, treatment, and genotype×treatmentinteraction for a suite of reproduction-related traits, includingrosette mass, inflorescence height, lateral branch number and fruitnumber. A second MANOVA was performed using data only from the threeblocks for which the seed number per fruit and total seed productionwere calculated. The second MANOVA included the following responsevariables: rosette mass, inflorescence height, lateral branch number,fruit number, seed number per fruit and total seed production.Univariate ANOVAs were performed following the MANOVAs in order todetermine which traits showed significant variation for phenotypicplasticity (genotype×treatment interaction). Flowering time was analyzedusing ANOVA only. For both the multivariate and univariate analyses, thesplit-plot experimental design required that the whole-plot factor,treatment, be tested over the whole-plot random error term,treatment×block. Genotype and genotype×treatment interaction were testedover the residual error. Data and residuals were examined to ensure thatall ANOVA assumptions were satisfied. Fruit number and total seedproduction required transformation (square root) in order to satisfyANOVA assumptions of normality and stable variance. Square roottransformation was used, because it is the recommended method fornormalizing counted data (Kuehl, 2000) and was the most effectivetransformation for meeting the ANOVA assumptions. The sequentialBonferroni correction was applied to the univariate P values to minimizeinflation of table-wide error from multiple tests (Rice, 1989).

To determine whether G-protein mutants showed significantly differentplasticities relative to Col, contrasts were performed using SAS 9.1 totest a priori-selected comparisons on all traits which had a significantgenotype×water level interaction. Because two alleles of each mutantwere studied, the contrasts were designed to simultaneously test theplasticity of Col against the plasticities of both mutant alleles ofeach gene. Combining alleles limited the inflation of a and, at the sametime, increased the biological validity of the experiment: if the twomutant alleles of the same gene showed divergent responses,statistically significant differences with Col would probably not bedetected. However, reaction norms were also examined individually toensure that alleles of the same gene had similar plasticity responses.

The following contrasts were performed for the univariate analyses: Colagainst both alleles combined for gpa1, agb1 and gcr1 mutants for amplewater vs moderate drought and ample water vs severe drought. The doublemutant gpa1-4agb1-2 was tested against Col, and against both allelescombined of gpa1 or agb1 for ample water vs moderate drought and amplewater vs severe drought. The sequential Bonferroni correction wasapplied to adjust for the inflation of type 1 error and to maintain atable-wide a of 0.05 (Rice, 1989). It has been suggested that thesequential Bonferroni correction can be overly stringent when applied toecological experiments; therefore, we also applied biological reasoningwhen interpreting each contrast (Moran, 2003). Because relative fitness(Stanton & Thiede, 2005) was a post hoc addition to our analysis,relative fitness was analyzed independently from the other responsevariables. ANOVA was performed to test whether genotype, treatment andgenotype by treatment interaction were significant.

Results Variation for Plasticity Among Genotypes (Genotype×EnvironmentInteractions)

Both MANOVAs showed that there is significant genotype×treatmentinteraction (Tables 1 and 2) for the reproduction-related traits (both Pvalues were <0.0001). Significant genotype and treatment effects werealso observed; however, the treatment effect for the seven variableMANOVA performed on only three blocks (Table 2) could not be estimatedas a result of insufficient error degrees of freedom. The MANOVAsindicated that significant genetic variation exists for reproductivetrait plasticity. Univariate ANOVAs were then performed in order todetermine which specific traits showed significant genotype×treatmentinteraction. The results from the univariate ANOVAs are shown in Table3. We found significant genotype×environment interactions for alltraits, even after the sequential Bonferroni correction was applied tothe P values. Least-squares means and standard errors are listed for allalleles and water levels in Table S1 (see Supporting Information). Ftests of specific contrasts between any of the G-protein mutants and Colfor ample water vs moderate drought and ample water vs severe droughtrevealed that, for rosette mass, number of lateral branches, total seedproduction and flowering time, there were no significant differences ingenotype×water level interactions (plasticities) after the applicationof the sequential Bonferroni correction (Table 4). However, significantdifferences in plasticities were observed between Col and the G-proteinmutants for a number of reproduction-related traits (Table 4). Althoughthe contrasts were performed on pooled alleles, reaction norms formutant alleles of the same gene were examined in cases in which thecontrasts were significant; such examination confirmed that both allelesof each gene did indeed show similar responses for all plasticity traitsdiscussed here (see, for example, Figs S4-S7; Supporting Information).Interestingly, agb1 mutants showed significantly reduced plasticitiesrelative to Col for inflorescence height (FIG. 3), fruit number (FIG. 4)and seeds per fruit (FIG. 5), suggesting that AGB1 functions as aplasticity gene, mediating phenotypic plasticity in the reproductivephase of plant growth in response to water availability. Theplasticities of the gpa1-4 agb1-2 double mutant for the most partresembled those of the single agb1 mutants. The exception was theinflorescence height, for which agb1 mutants showed significantlyreduced plasticity relative to the double mutant (FIG. 3, Table 4). gpa1mutants showed increased plasticity for inflorescence height relative toCol (FIG. 3). The double mutant showed reduced plasticity relative togpa1 for inflorescence height (FIG. 3), indicating that the doublemutant shows an intermediate phenotype. gcr1 mutants showed increasedplasticity for square root fruit number relative to the wild-type (FIG.4).

For total seed production, no significant differences were found in theplasticities of Col and any of the G-protein mutants following thesequential Bonferroni correction (Table 2). However, it should be notedthat, before statistical correction, contrasts between Col and agb1 inample water vs moderate drought (P=0.0027) and ample water vs severedrought (P=0.003) were significant. Given that two independent allelesof agb1 were used in the experiment and their reaction norms showedreduced plasticity for total seed production (FIG. 6; see also Fig. S7,Supporting Information) relative to Col, and also that the sequentialBonferroni correction can be overly conservative (Moran, 2003), we feelconfident that AGB1 also mediates plasticity for total seed production.All G-protein mutants showed reduced fitness, defined here as total seedproduction, under ample water conditions, but the agb1 mutants and thedouble mutant gpa1agb1 showed increased fitness under both moderate andsevere drought stress relative to Col (FIG. 6). The relative fitnessdata also corroborate rank changing among the genotypes in differentenvironments (FIG. 7). A significant genotype effect (P<0.0001) andsignificant genotype×treatment interaction (P=0.0009) were observed forrelative fitness. Although all mutant genotypes showed reduced relativefitness relative to Col under ample water growth conditions, agb1mutants and the double mutant gpa1-4agb1-2 showed increased relativefitness relative to Col under drought stress.

Phenotypic Variance of within x Treatment Trait Means

The within-treatment, experiment-wide variances of the trait means forthe mutants and wild-type for ample water and severe drought treatmentsare shown in Table S2 (see Supporting Information). Equal variance testswere performed to determine whether the mutants showed increased ordecreased phenotypic variation relative to the wild-type within aparticular environment (Table S3). After correcting for multiple F testsusing the sequential Bonferroni correction, only one null hypothesis wasrejected. agb1-2 mutants showed significantly reduced variance(P<0.0005) for seed number per fruit under ample water relative to thewild-type. However, this reduction in variance was not observed in thesecond agb1 allele, agb1-1 (P=0.168), which brings into question thebiological relevance of this statistically significant observation.Overall, phenotypic variance for traits within a given environment wasnot impacted significantly by G-protein mutations.

Discussion AGB1 Functions as a Plasticity Gene for a Number ofReproduction-Related Traits

Our data show that mutation of the sole Gβ subunit of Arabidopsis, AGB1,results in pleiotropic effects on the extent of plasticity in responseto water availability. agb1 mutants showed reduced plasticity for thenumber of fruits, inflorescence height, seed number per fruit and totalseed production relative to Col. Interestingly, agb1 mutants showedincreased seed production per fruit under drought stress relative to thewild-type, and reduced seed production per fruit relative to thewild-type under well-watered conditions. The reduced plasticity of agb1mutants resulted in enhanced fitness under drought stress, but wasmaladaptive under well-watered conditions. This conclusion was alsosupported when relative fitness was assessed. All G-protein mutants,that showed reduced plasticity for reproductive traits, including agb1,showed lower relative fitness relative to Col under ample waterconditions. Under drought stress, agb1 mutants and the double mutantshowed increased relative fitness relative to Col. The relative fitnessdata support the conclusion that the significant genotype×treatmentinteraction observed for total seed production can be attributed to rankchanging among the genotypes, and is not a consequence of changes invariance or the square root transformation. It has also been noted thatdifferences in phenotypic variation can be a consequence of age- orsize-dependent ontogenetic drift (McConnaughay & Coleman, 1999). Itshould be noted that we observed no significant differences in rosettegrowth rate (as determined by projected leaf area calculations) amongthe genotypes within a given water treatment (Figs S1-S3, see SupportingInformation), suggesting that the significant variation for plasticityobserved cannot be attributed to ontogenetic drift. These resultssuggest that AGB1 is a plasticity gene, as it contributes to the shapeof the phenotypic response under the environments tested in ourexperiment.

Multiple alleles have not been used frequently in mutant studies ofphenotypic plasticity; one exception is the study by Galen et al.(2004). The use of two independent mutant alleles of agb1 in this studystrengthens our conclusion that AGB1 functions as a plasticity gene, atleast in the environments tested. These results suggest that it would beworthwhile to pursue additional experiments to determine the extent towhich G proteins function in regulating phenotypic plasticity underdifferent stresses and in natural environments, where other resourcelimitations might influence the extent of plasticity observed. It hasbeen recognized that there may also be costs associated with plasticityunder some circumstances (Callahan et al., 2005; Ghalambor et al., 2007;Van Buskirk & Steiner, 2009). Although additional research underdifferent environments is required, plasticity costs may be illustratedunder our conditions by the fact that, under water limitation, the leastplastic genotype, agb1, showed greater fitness (by both absolute andrelative measures) than the more plastic genotypes.

AGB1 has been shown previously to function in inflorescence and fruitdevelopment. agb1-1 was originally isolated in a screen for erecta-likemutations, where it showed a slightly reduced inflorescence height andsignificantly shortened, blunt-tipped fruits relative to the wild-type,phenotypes which were later also observed in agb1-2 (Lease et al., 2001;Ullah et al., 2003). In addition, it was shown that AGB1 was expressedubiquitously throughout the plant, but its expression was elevated inflowers and highest in fruits (Lease et al., 2001). The shortened fruitphenotype corresponds to our findings that agb1 shows reduced seeds perfruit. This short phenotype is specific to agb1 mutants and is notobserved in gpa1, agg1 and agg2 mutants (Ullah et al., 2003; Trusov etal., 2008). Functional selectivity of the Gβ subunit has been reportedfor other G-protein-mediated responses, including necrotrophic pathogenresistance (Llorente et al., 2005; Trusov et al., 2006), sugarinhibition of seed germination and lateral root formation (Chen et al.,2006).

According to the paradigm of G-protein signaling, activation of GPA1results in a conformational change in Gα and the release of the Gβγdimer, and signal propagation. As the reduced plasticity phenotype ispresent in agb1 mutants and in gpa1agb1 double mutants, but not in gpa1mutants, we can conclude that Gβ is responsible for signal integrationor transduction, resulting in wild-type plasticity for the number offruits, seed number per fruit and total seed production. In classicalG-protein signaling, the a subunit typically requires the β subunit, notonly for trimer reassembly, but also for GPCR association. Therefore,GPA1 activation is eliminated by both gpa1 and agb1 mutations, but AGB1activation is abolished only by the agb1 mutation. For inflorescenceheight, gpa1 and agb1 display opposite phenotypes (enhanced and reducedplasticity, respectively), which also suggests that AGB1 is responsiblefor mediating wild-type plasticity, as free AGB1 is active in gpa1mutants (potentially more so than in the wild-type), but is absent fromagb1 mutants. gcr1 mutants showed increased plasticity relative to thewild-type for fruit number and, although GCR1 might function in themediation of plasticity for fruit number, there are probably additionalunknown GPCRs that contribute to the perception and/or integration ofenvironmental input signals with regard to the regulation of phenotypicplasticity.

G-Protein Mutations do not Affect Significantly the Level of PhenotypicVariation within an Environment

Within a given environment, genetically identical organisms can showdivergent phenotypes as a result of stochasticity in gene expression.These random events among cellular molecules can modify cell status andconsequently result in phenotypic changes at the organismal level (oftenthought of as experimental ‘noise’). Stochasticity is generally thoughtto be detrimental to fitness; however, it can also be a source ofheterogeneity, which can provide a fitness benefit in fluctuatingenvironments (Kaern et al., 2005; Raser & O'Shea, 2005). A G-proteinmutation might increase or decrease the ability of a cell to bufferitself against stochasticity, and therefore it has been hypothesizedthat G-protein mutations might affect the amount of phenotypic variationwithin an environment (Assmann, 2004). To test this hypothesis, wecompared the phenotypic variances (Table S2) of the G-protein mutantswithin an environment with the phenotypic variance of the wild-typewithin the same environment. We found that the within-environmentphenotypic variation was not altered significantly by mutations inG-protein subunit genes (Table S3, Supporting Information), suggestingthat this hypothesis is not supported: G-protein mutations do not affectthe range of possible phenotypes within our environments.

agb1 Mutants Show Enhanced Fitness Under Drought Stress

Based on their previously reported altered stomatal sensitivities to ABA(Wang et al., 2001; Pandey & Assmann, 2004; Fan et al., 2008), it ispossible to make predictions concerning the fitness benefits or coststhat G-protein mutants may incur when grown under drought stressconditions. However, although gpa1 and agb1 are hyposensitive withregard to the ABA inhibition of stomatal opening, but show wild-type ABApromotion of stomatal closure (Wang et al., 2001; Fan et al., 2008), andgcr1 mutants are hypersensitive towards both ABA inhibition of stomatalopening and promotion of closure (Pandey & Assmann, 2004), our detailedphenotypic analysis of whole-plant traits under controlled water stressconditions did not support the predictions that would be made based onthese stomatal response phenotypes. gcr1 mutants, despite their stomatalhypersensitivity to ABA and their reported improved recovery followingdrought stress (Pandey & Assmann, 2004), showed no fitness advantagerelative to the wild-type under drought stress or well-wateredconditions. Although we predicted that gpa1 and agb1 mutants would showreduced fitness under drought stress based on the partial ABAinsensitivity of their stomatal phenotypes, agb1 mutants (but not gpa1mutants) exhibited increased fitness under drought stress and reducedfitness under well-watered conditions. The pleiotropic nature ofG-protein mutations may, in part, explain why the stomatal responsephenotypes were not predictive of plant fitness under drought stress.Recently, it has been shown that G proteins regulate stomatal density,GPA1 as a positive modulator and AGB1 as a negative regulator (Zhang etal., 2008a), which may have implications for water loss and carbonassimilation under different environmental conditions. In addition, agb1mutants and, to a lesser degree, gpa1 mutants are hypersensitive to ABAinhibition of germination and root growth (Pandey et al., 2006), whichmay contribute to survival under drought stress. Nevertheless, althoughthe lack of plasticity of agb1 in reproductive-related traits resultedin a fitness advantage under drought stress, lack of plasticity wasmaladaptive for agb1 under well-watered conditions. Therefore, Gproteins do contribute to plant fitness, in part via the regulation ofphenotypic plasticity. Given that climate change can lead to increasedvariability in environments and resources, this finding could haveimportant agronomical implications, as agb1 mutants show reducedplasticity and therefore more stable yields across environments.

Conclusion

Phenotypic analysis of G-protein mutants under multiple environmentalconditions has identified novel functions of plant heterotrimeric Gproteins in the regulation of the phenotypic plasticity of inflorescenceheight, seed number per fruit, fruit number and total seed production.We also found that the known altered guard cell sensitivities towardsABA did not predict the fitness outcomes of the mutants under droughtstress. All G-protein mutants studied showed reduced fitness underwell-watered as well as drought environments, with the exception ofagb1-containing mutants which showed improved fitness under droughtstress conditions. These results thus attest to one of the apparentparadoxes of plant G-protein signaling: although G-protein mutation isnot lethal, it does, in fact, result in nonoptimal phenotypes under someenvironmental conditions.

G proteins mediate responses to ABA, auxin, brassinosteroids,gibberellins and sugars, environmental signals, including ozone andpathogens, and intrinsic, unknown developmental cues mediating leafshape, stomatal density and fruit shape. A fundamental question inG-protein signaling is how only two heterotrimeric G-proteincombinations (GPA1/AGB1/AGG1 and GPA1/AGB1/AGG2) can transduce such adiversity of signals. Our results, implicating heterotrimeric G proteinsin the mediation of phenotypic plasticity responses, support the modelthat G proteins function, at least in part, as cross-talk hubs,integrating signals, rather than directly transducing them (Assmann,2004), thereby tweaking a phenotype relative to the environment at hand.More studies are warranted in which G-protein regulation of plasticityis examined across additional environmental gradients, as well as acrossgenerations, in order to further elucidate this novel contribution ofheterotrimeric G proteins to plant development and fitness. It will beinteresting to assess the extent to which the results presented herewould extrapolate to field studies: studies in highly controlledenvironments are important steps towards the design of such experiments.Although QTL-based studies have supported the existence of plasticitygenes, the present study is one of a few that has directly tested theregulation of phenotypic plasticity by specific genes. Additionalplasticity studies with other environmental signaling mutants will beintegral to our understanding of whether plasticity genes are rare orcommon in plant and other genomes, and to gaining an insight into thegenetic basis of phenotypic plasticity.

TABLE 1 Wilks' lambda, F and P values from multivariate analysis ofvariance (MANOVA) including the following response variables: rosettemass, inflorescence height, number of lateral branches and square rootnumber of fruits; data from all 12 experimental blocks Wilks'Denominator Effect lambda F value Numerator d.f. d.f. P value Genotype0.0419 41.48 28 823.49 <0.0001 Treatment 0.0056 58.65 8 38 <0.0001Genotype × 0.2046 8 56 889.04 <0.0001 treatment

TABLE 2 Wilks' lambda, F and P values from multivariate analysis ofvariance (MANOVA) including the following response variables: rosettemass, inflorescence height, number of lateral branches and square rootnumber of fruits; seed number per fruit and square root total seedproduction; data from the three experimental blocks for which seednumber per fruit was obtained Wilks' Numerator Denominator Effect lambdaF value d.f. d.f. P value Genotype 0.0053¹ 8.65¹ 42¹ 177¹ <0.0001¹Treatment Genotype × 0.0208 2.54 84 212.6 <0.0001 treatment¹Multivariate analysis of the significance of the treatment effect couldnot be performed because of insufficient error d.f. (treatment × blockis the appropriate error term given the split-plot experimental design).

TABLE 3 F and (P values) for all fixed effects for univariate analysesof variance (ANOVAs); treatment was tested over the treatment × blockerror term, and geotype and genotype × treatment were tested over theresidual error; all P values were significant before and aftersequential Bonferroni correction Effect Genotype × Response VariableGenotype Treatment treatment Rosette mass 28.08 (≦0.0001) 744.91(≦0.0001) 8.43 (≦0.0001) Inflorescence height 40.89 (≦0.0001)  541.7(≦0.0001) 12.79 (≦0.0001)  Number of lateral branches 108.9 (<0.0001) 272.7 (≦0.0001) 12.79 (≦0.0001)  Square root number of fruits  9.35(≦0.0001) 320.91 (≦0.0001)   13 (≦0.0001) Seeds per fruit¹ 10.47(≦0.0001)  256.7 (≦0.0001) 4.23 (≦0.0001) Seed production¹  7.79(≦0.0001) 220.07 (≦0.0001) 2.88 (≦0.0041) Flowering time 50.37 (≦0.0001)12.7117323 (0.0002)      3.23 (0.0001)    ¹Only three blocks were usedto assess seeds per fruit and seed production.

TABLE 4 P values of univariate contrasts on genotype x treatment (ample,ample water, moderate, moderate drought severe, severe drought) TotalInflores- No. Seeds seed Flower- Rosette cence lateral Sq. rt. per pro-ing Response variable mass height branches no. fruit fruit¹ duction¹Time Contrast Col vs both agb1 ample 0.0137 0.0001 0.104 ≦ 0.0001 0.00030.0027 0.9828 vs moderate Col vs both agb1 ample 0.002 0.0022 0.01830.0091 ≦ 0.0001 0.003 0.645 vs severe Col vs double ample vs 0.00170.472 0.0876 ≦ 0.0001 0.0052 0.0323 0.8351 moderate Col vs double amplevs 0.002 0.2793 0.1045 0.1331 0.0049 0.0715 0.3148 severe Col vs bothgcr1 ample 0.9661 0.8617 0.882 0.0024 0.7164 0.7598 0.5887 vs moderateCol vs both gcr1 ample 0.2308 0.1975 0.4888 ≦ 0.0001 0.1723 0.84040.0859 vs severe Col vs both gpa1 ample 0.3071 0.0007 0.1035 0.72620.5187 0.8318 0.496 vs moderate Col vs both gpa1 ample 0.0301 ≦ 0.00010.0844 0.2792 0.1083 0.2709 0.0019 vs severe Double vs both agb1 0.23990.0024 0.7284 0.5487 0.5548 0.5354 0.8268 ample vs moderate Double vsboth agb1 0.6283 ≦ 0.0001 0.6209 0.3752 0.3024 0.3139 0.1056 ample vssevere Double vs both gpa1 ≦ 0.0001 ≦ 0.0001 0.7291 ≦ 0.0001 ≦ 0.00020.0083 0.6594 ample vs moderate Double vs both gpa1 ≦ 0.0001 ≦ 0.00010.882 0.0051 0.0812 0.3138 0.0483 ample vs severe ¹Data from threeblocks only. Values in bold were significant before application of thesequential Bonferroni correction; values in italic and with underlineswere significant after application of the Bonferroni correction.

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RGA1 vs d1

Genbank RGA1 cDNA sequence:

Accession: D38232 GI: 540532

RGA1 coding region sequence: SEQ ID NO: 1ATGGGCTCATCCTGTAGCAGATCTCATTCTTTAAGTGAGGCTGAAACAACCAAAAATGCAAAATCTGCAGACATTGACAGGCGAATTTTGCAAGAGACAAAAGCAGAGCAACACATCCACAAGCTCTTACTTCTTGGTGCGGGAGAATCAGGGAAGTCTACGATATTTAAACAGATTAAGCTCCTTTTCCAAACTGGCTTTGATGAGGCAGAACTTAGGAGCTACACATCAGTTATCCATGCAAACGTCTATCAGACAATTAAAATACTATATGAAGGAGCAAAAGAACTCTCACAAGTGGAATCAGATTCCTCAAAGTATGTTATATCCCCAGATAACCAGGAAATTGGAGAAAAACTATCAGATATTGATGGCAGGTTGGATTATCCACTGCTGAACAAAGAACTTGTACTCGATGTAAAAAGGTTATGGCAAGACCCAGCCATTCAGGAAACTTACTTACGTGGAAGTATTCTGCAACTTCCTGATTGTGCACAATACTTCATGGAAAATTTGGATCGATTAGCTGAAGCAGGTTATGTGCCAACAAAGGAGGATGTGCTTTATGCAAGAGTACGGACAAATGGTGTTGTACAAATACAATTTAGTCCTGTTGGAGAAAACAAAAGAGGTGGAGAGGTATATAGGTTGTATGATGTAGGAGGCCAGAGGAATGAGAGGAGAAAGTGGATTCATCTTTTTGAAGGTGTTAATGCGGTAATCTTTTGTGCTGCCATTAGCGAATATGATCAGATGCTATTTGAAGATGAGACAAAAAACAGAATGATGGAGACCAAGGAACTCTTTGACTGGGTTTTAAAGCAAAGATGTTTTGAGAAAACATCATTCATTCTGTTTCTCAACAAATTTGATATATTCGAGAAGAAAATACAAAAGGTTCCTTTAAGTGTGTGCGAGTGGTTTAAAGACTACCAGCCTATTGCACCTGGGAAACAGGAGGTTGAACATGCATATGAGTTTGTCAAGAAGAAGTTTGAAGAGCTCTACTTCCAGAGCAGCAAGCCTGACCGTGTGGACCGCGTCTTCAAAATCTACAGAACTACGGCCCTAGACCAGAAACTTGTAAAGAAGACATTCAAGTTGATTGATGAGAGCATGAGACGC TCCAGGGAAGGAACTTGAd1 coding region sequence (from our cDNA sequencing) SEQ ID NO 2ATGGGCTCATCCTGTAGCAGATCTCATTCTTTAAGTGAGGCTGAAACAACCAAAAATGCAAAATCTGCAGACATTGACAGGCGAATTTTGCAAGAGACAAAAGCAGAGCAACACATCCACAAGCTCTTACTTCTTGGTGCGGGAGAATCAGGGAAGTCTACGATATTTAAACAGATTAAGCTCCTTTTCCAAACTGGCTTTGATGAGGCAGAACTTAGGAGCTACACATCAGTTATCCATGCAAACGTCTATCAGACAATTAAAATACTATATGAAGGAGCAAAAGAACTCTCACAAGTGGAATCAGATTCCTCAAAGTATGTTATATCCCCAGATAACCAGGAAATTGGAGAAAAACTATCAGATATTGATGGCAGGTTGGATTATCCACTGCTGAACAAAGAACTTGTACTCGATGTAAAAAGGTTATGGCAAGACCCAGCCATTCAGGAAACTTACTTACGTGGAAGTATTCTGCAACTTCCTGATTGTGCACAATACTTCATGGAAAATTTGGATCGATTAGCTGAAGCAGGTTATGTGCCAACAAAGGAGGATGTGCTTTATGCAAGAGTACGGACAAATGGTGTTGTACAAATACAATTTAGTCCTGTTGGAGAAAACAAAAGAGGTGGAGAGGTATATAGGTTGTATGATGTAGGAGGCCAGAGGAATGAGAGGAGAAAGTGGATTCATCTTTTTGAAGGTGTTAATGCGGTAATCTTTTGTGCTGCCATTAGCGAATATGATCAGATGCTATTTGAAGATGAGACAAAAAACAGAATGATGGAGACCAAGGAACTCTTTGACTGGGTTTTAAAGCAAAGATGTTTTGAGAAAACATCATTCATTCTGTTTCTCAACAAATTTGATATATTCGAGAAGAAAATACAAAAGGTTCCTTTAAGTGTGCGAGTGGTTTAAAGACTACCAGCCTATTGCACCTGGGAAACAGGAGGTTGAACATGCATATGAGTTTGTCAAGAAGAAGTTTGAAGAGCTCTACTTCCAGAGCAGCAAGCCTGACCGTGTGGACCGCGTCTTCAAAATCTACAGAACTACGGCCCTAGACCAGAAACTTGTAAAGAAGACATTCAAGTTGATTGATGAGAGCATGAGACGCTC CAGGGAAGGAACTTGAGenbank RGA1 protein sequence:

Accession: BAA07405 GI: 540533

RGA1 protein sequence: SEQ ID NO: 3MGSSCSRSHSLSEAETTKNAKSADIDRRILQETKAEQHIHKLLLLGAGESGKSTIFKQIKLLFQTGFDEAELRSYTSVIHANVYQTIKILYEGAKELSQVESDSSKYVISPDNQEIGEKLSDIDGRLDYPLLNKELVLDVKRLWQDPAIQETYLRGSILQLPDCAQYFMENLDRLAEAGYVPTKEDVLYARVRTNGVVQIQFSPVGENKRGGEVYRLYDVGGQRNERRKWIHLFEGVNAVIFCAAISEYDQMLFEDETKNRMMETKELFDWVLKQRCFEKTSFILFLNKFDIFEKKIQKVPLSVCEWFKDYQPIAPGKQEVEHAYEFVKKKFEELYFQSSKPDRVDRVFKIYRTTALDQK LVKKTFKLIDESMRRSREGT-d1 predicted protein sequence (based on our cDNA sequencing)SEQ ID NO: 4 MGSSCSRSHSLSEAETTKNAKSADIDRRILQETKAEQHIHKLLLLGAGESGKSTIFKQIKLLFQTGFDEAELRSYTSVIHANVYQTIKILYEGAKELSQVESDSSKYVISPDNQEIGEKLSDIDGRLDYPLLNKELVLDVKRLWQDPAIQETYLRGSILQLPDCAQYFMENLDRLAEAGYVPTKEDVLYARVRTNGVVQIQFSPVGENKRGGEVYRLYDVGGQRNERRKWIHLFEGVNAVIFCAAISEYDQMLFEDETKNRMMETKELFDWVLKQRCFEKTSFILFLNKFDIFEKKIQKVPLSVRVV-MSU Rice Genome Annotation Project LOC_Os05g26890 (RGA1) genomicsequence (Oryza sativa ssp japonica cv. Nipponbare—Sequence Release 7)Sequence aligns 100% with the RGA1 sequence found within genbank clones:Chromosome 5 clone OSJNBa0049D13 (accession AC144739)Chromosome 5 clone OJ1005_D04 (accession AC117264)

RGA1 genomic sequence: SEQ ID NO: 5ATGGGCTCATCCTGTAGCAGATCTCATTCTTTAAGTGAGGCTGAAACAACCAAAAATGCAAAAGTAAGTTAGCACTCGGACTTATTGAACAAGTAAATGCTAACTCAATTCTTGATTTGAGAGTTGCCACATTTGGTTTCTTCTAATTCAGCTGGTAACAGTCTGCAGACATTGACAGGCGAATTTTGCAAGAGACAAAAGCAGAGCAACACATCCACAAGCTCTTACTTCTTGGTATTGCTAACTTTCCCAAATTTAAGTGGTCATTTTCCTTGTCACAATTATCTGTGCTACCTTTAGTATCTATTGGTTCAGAAAATTAATTGTTTATGTTGTTCCTATTTACCTCTATAAAAAAACCTTTCTCATGTTATTTCCAAAAAAAAAGAAGATAAATAAATGTATCCTAGAAATTTTTAGTTTGAACTTGTTCTCAATGTGGATCCATCCTTCTTTCTCTCTCTCAATTGCTTCTGTTTTAAGGTGCGGGAGAATCAGGGAAGTCTACGATATTTAAACAGGTGATGAATGTTATATTCCATGGAGAATCATAATCCGTACGCCGCTAGTTAGTCTGATGTATTCTTACTGTTCACCTGCAGATTAAGCTCCTTTTCCAAACTGGCTTTGATGAGGCAGAACTTAGGAGCTACACATCAGTTATCCATGCAAACGTCTATCAGACAATTAAAGTATGCAATACTGGAAAGGGTGTGTCTTTTTTTTCTTATTGCAAAGTGGGGATTATGTAGGAGATTCGACTAGGGATTTGTATTCTGTTCATAAGGAAATGCGTTCATACTTTTCCTTTTTGTCGAGTAATGTGTTAAATGTTAACAGATACTATATGAAGGAGCAAAAGAACTCTCACAAGTGGAATCAGATTCCTCAAAGTATGTTATATCCCCAGATAACCAGGTTTGTGCTTACTCTTTACTCAACAGTTAAAGCTAAATCTGTGCATATGAACATGTCTTGTTAAATCTGGGAATACAAACATTTTGATTTGCAACATTTCTGTTGTAGTCAAGCTGCTCGGCTCTATGTTTTAACCTGTTAAGACCTTGTAGACTGTGCTCGGCTCTATTGTAGTCTTATATTTTACACGGTCATTCTATAATGAAAACTTGAAAAAGATATCTATTGAACCGTACAATGTACTGAACAAAGTAGAAAAGAACAATGAGATTTTGTAACATTTATTCTTCCTTGTTTATTTGATTGCTTCAGACAATTGTTGATATGCTAAAAATAACTTGGTATCAAATGTGGGTGTTATAAGATTCAATTTTTTTCTCAACCAGGTTAAAAAAAGTATACCTTTGTGCATTTACCTTGTTCCGTTGCTTTGGAACTTTAAAGGAAAACTGACTTTTCTTAGGCATTGAAAGACAAATATCACCAGTTTCACACTGTACACCTTACCAACCAATTTTGTTTCTTAGATGTCATTTACTTTGTCATATCATCAGGAAATTGGAGAAAAACTATCAGATATTGATGGCAGGTTGGATTATCCACTGCTGAACAAAGAACTTGTACTCGATGTAAAAAGGTTATGGCAAGACCCAGCCATTCAGGTGAAAACAAATAGCCATTCAAATCTTTTGAAGTTATATAGTTTTCCTGGCCAGGTGTGCTGAAGCAATGCTCTATACTGTAGGAAACTTACTTACGTGGAAGTATTCTGCAACTTCCTGATTGTGCACAATACTTCATGGAAAATTTGGATCGATTAGCTGAAGCAGGTTATGTGCCAACAAAGGTGTGCTGTCCATGTTCATAGACAATTATTTACATATTCTCAGATATTTGTGCTGACACCATTTCATGTTGATTTTTAGTCTACTTAGTCAGAGGTTGTCAAATGGTTAACTATGTGTACTGAGTCAGAGGTTGCCAAATAGTTTTAAAAGATGGGCATATGTTTATCCTTATCTTTTAAATAATATTGGAGGCTATCCTTTAAAATTCAATATTAGGGAGGAGAAACTATTATTCTACCGTTATTACGCAGTCTACATAACGAAGGTAAAAAATGTCCCTGTGAAACATAGGGTGCAAAACTGCTGTGAATAAAACTCTACTTATCTAAGCACCTTGAGCTTTTGAGTTCCCACATATTAATCTTATGACACTAGCATATATTTTTTTTGTTCAGTTCCTTCAATAAGTTGCAAACCACAAATATGATCACTGTACCATCCACTTTTGCAACCATTTCCCGTCATTTCTTAAGCATAGAAAATTGTTTGTCACTTGTTTAAGTCCACACTGCATCAAAATTCCAATTAACATTGTGTGTGCTAAGTGAAGATATGACTCCATATTTCTGCATTTAGCAGTCTGATGGATAATTTGTGATTGTACCTTGTCTAATGGTTCGTTTGAAAGGCTGGTAGTTGATCTTCCATACTTAAGAATGCTTGCAGTATTATAGTTGTCAATATTATGAGTCATTTTGCAGGAGGATGTGCTTTATGCAAGAGTACGGACAAATGGTGTTGTACAAATACAATTTAGGTAATCTGCTGACACTATTTTTTGCACATTTTTTTGCTGGTTGCTCTACTATGTACAGAACGACAAGTTGAAGTCCTTTTTTTCTCCCCTTTCACTTCTAAGATATGACCTGAGAGGTTCTGAATGTAGCTGTTTTAAGATGAGTTGAATCATCTAGTTAACTGGGTTTCTTTCTGCAGTCCTGTTGGAGAAAACAAAAGAGGTGGAGAGGTATATAGGTTGTATGATGTAGGAGGCCAGAGGAATGAGAGGAGAAAGTGGATTCATCTTTTTGAAGGTGTTAATGCGGTAATCTTTTGTGCTGCCATTAGCGAGTAAGTACAATTTTTTTGATTGTTGAACTTATCCTAATCTGCTAAGTTCTTCTCATAGGCTTCTTGTTCATTTCAGATATGATCAGATGCTATTTGAAGATGAGACAAAAAACAGAATGATGGAGACCAAGGAACTCTTTGACTGGGTTTTAAAGCAAAGATGTTTTGAGGTCTGCATGCATCCATCTCTGCAACCTTTGTGCTCATGCTTTTTTTCTCATTTTGAAACTAATTACGGTGCTATATTGACCATCAGAAAACATCATTCATTCTGTTTCTCAACAAATTTGATATATTCGAGAAGAAAATACAAAAGGTAAGGCCTGCTCTTTGTACCAATGCATAGTTTAGTACTAAATGTTACCAACATTTATGTTTACGCTGGTTACGTAGGTTCCTTTAAGTGTGTGCGAGTGGTTTAAAGACTACCAGCCTATTGCACCTGGGAAACAGGAGGTTGAACATGCATATGAGTGAGTGCACTACTCGCCCTCTCAGATGAACATGGGCATTTGGCCATTTGTAATGTTGCTGCATGGTGCACTTATATGCCTTGATAAGTTTTTCCATTCTAATGTTATATAGTATCAAACGTTCATCATTACTGTGGCTTATGGTCTGGAGTGACGTTTTACAGGTTTGTCAAGAAGAAGTTTGAAGAGCTCTACTTCCAGAGCAGCAAGCCTGACCGTGTGGACCGCGTCTTCAAAATCTACAGAACTACGGCCCTAGACCAGAAACTTGTAAAGAAGACATTCAAGTTGATTGATGAGAGCATGAGACGCTCCAGGGAAGGAACTTGAd1 allele sequence (from our genomic DNA sequencing) SEQ ID NO: 6ATGGGCTCATCCTGTAGCAGATCTCATTCTTTAAGTGAGGCTGAAACAACCAAAAATGCAAAAGTAAGTTAGCACTCGGACTTATTGAACAAGTAAATGCTAACTCAATTCTTGATTTGAGAGTTGCCACATTTGGTTTCTTCTAATTCAGCTGGTAACAGTCTGCAGACATTGACAGGCGAATTTTGCAAGAGACAAAAGCAGAGCAACACATCCACAAGCTCTTACTTCTTGGTATTGCTAACTTTCCCAAATTTAAGTGGTCATTTTCCTTGTCACAATTATCTGTGCTACCTTTAGTATCTATTGGTTCAGAAAATTAATTGTTTATGTTGTTCCTATTTACCTCTATAAAAAAACCTTTCTCATGTTATTTCCAAAAAAAAAGAAGATAAATAAATGTATCCTAGAAATTTTTAGTTTGAACTTGTTCTCAATGTGGATCCATCCTTCTTTCTCTCTCTCAATTGCTTCTGTTTTAAGGTGCGGGAGAATCAGGGAAGTCTACGATATTTAAACAGGTGATGAATGTTATATTCCATGGAGAATCATAATCCGTACGCCGCTAGTTAGTCTGATGTATTCTTACTGTTCACCTGCAGATTAAGCTCCTTTTCCAAACTGGCTTTGATGAGGCAGAACTTAGGAGCTACACATCAGTTATCCATGCAAACGTCTATCAGACAATTAAAGTATGCAATACTGGAAAGGGTGTGTCTTTTTTTTCTTATTGCAAAGTGGGGATTATGTAGGAGATTCGACTAGGGATTTGTATTCTGTTCATAAGGAAATGCGTTCATACTTTTCCTTTTTGTCGAGTAATGTGTTAAATGTTAACAGATACTATATGAAGGAGCAAAAGAACTCTCACAAGTGGAATCAGATTCCTCAAAGTATGTTATATCCCCAGATAACCAGGTTTGTGCTTACTCTTTACTCAACAGTTAAAGCTAAATCTGTGCATATGAACATGTCTTGTTAAATCTGGGAATACAAACATTTTGATTTGCAACATTTCTGTTGTAGTCAAGCTGCTCGGCTCTATGTTTTAACCTGTTAAGACCTTGTAGACTGTGCTCGGCTCTATTGTAGTCTTATGTTTTACACGGTCATTCTATAATGAAAACTTGAAAAAGATATCTATTGAACCGTACAATGTACTGAACAAAGTAGAAAAGAACAATGAGATTTTGTAACATTTATTCTTCCTTGTTTATTTGATTGCTTCAGACAATTGTTGATATGCTAAAAATAACTTGGTATCAAATGTGGGTGTTATAAGATTCAATTTTTTTCTCAACCAGGTTAAAAAAAGTATACCTTTGTGCATTTACCTTGTTCCGTTGCTTTGGAACTTTAAAGGAAAACTGACTTTTCTTAGGCATTGAAAGACAAATATCACCAGTTTCACACTGTACACCTTACCAACCAATTTTGTTTCTTAGATGTCATTTACTTTGTCATATCATCAGGAAATTGGAGAAAAACTATCAGATATTGATGGCAGGTTGGATTATCCACTGCTGAACAAAGAACTTGTACTCGATGTAAAAAGGTTATGGCAAGACCCAGCCATTCAGGTGAAAACAAATAGCCATTCAAATCTTTTGAAGTTATATAGTTTTCCTGGCCAGGTGTGCTGAAGCAATGCTCTATACTGTAGGAAACTTACTTACGTGGAAGTATTCTGCAACTTCCTGATTGTGCACAATACTTCATGGAAAATTTGGATCGATTAGCTGAAGCAGGTTATGTGCCAACAAAGGTGTGCTGTCCATGTTCATAGACAATTATTTACATATTCTCAGATATTTGTGCTGACACCATTTCATGTTGATTTTTAGTCTACTTAGTCAGAGGTTGTCAAATGGTTAACTATGTGTACTGAGTCAGAGGTTGCCAAATAGTTTTAAAAGATGGGCATATGTTTATCCTTATCTTTTAAATAATATTGGAGGCTATCCTTTAAAATTCAATATTAGGGAGGAGAAACTATTATTCTACCGTTATTACGCAGTCTACATAACGAAGGTAAAAAATGTCCCTGTGAAACATAGGGTGCAAAACTGCTGTGAATAAAACTCTACTTATCTAAGCACCTTGAGCTTTTGAGTTCCCACATATTAATCTTATGACACTAGCATATATTTTTTTTGTTCAGTTCCTTCAATAAGTTGCAAACCACAAATATGATCACTGTACCATCCACTTTTGCAACCATTTCCCGTCATTTCTTAAGCATAGAAAATTGTTTGTCACTTGTTTAAGTCCACACTGCATCAAAATTCCAATTAACATTGTGTGTGCTAAGTGAAGATATGACTCCATATTTCTGCATTTAGCAGTCTGATGGATAATTTGTGATTGTACCTTGTCTAATGGTTCGTTTGAAAGGCTGGTAGTTGATCTTCCATACTTAAGAATGCTTGCAGTATTATAGTTGTCAATATTATGAGTCATTTTGCAGGAGGATGTGCTTTATGCAAGAGTACGGACAAATGGTGTTGTACAAATACAATTTAGGTAATCTGCTGACACTATTTTTTGCACATTTTTTTGCTGGTTGCTCTACTATGTACAGAACGACAAGTTGAAGTCCTTTTTTTCTCCCCTTTCACTTCTAAGATATGACCTGAGAGGTTCTGAATGTAGCTGTTTTAAGATGAGTTGAATCATCTAGTTAACTGGGTTTCTTTCTGCAGTCCTGTTGGAGAAAACAAAAGAGGTGGAGAGGTATATAGGTTGTATGATGTAGGAGGCCAGAGGAATGAGAGGAGAAAGTGGATTCATCTTTTTGAAGGTGTTAATGCGGTAATCTTTTGTGCTGCCATTAGCGAGTAAGTACAATTTTTTTGATTGTTGAACTTATCCTAATCTGCTAAGTTCTTCTCATAGGCTTCTTGTTCATTTCAGATATGATCAGATGCTATTTGAAGATGAGACAAAAAACAGAATGATGGAGACCAAGGAACTCTTTGACTGGGTTTTAAAGCAAAGATGTTTTGAGGTCTGCATGCATCCATCTCTGCAACCTTTGTGCTCATGCTTTTTTTCTCATTTTGAAACTAATTACGGTGCTATATTGACCATCAGAAAACATCATTCATTCTGTTTCTCAACAAATTTGATATATTCGAGAAGAAAATACAAAAGGTAAGGCCTGCTCTTTGTACCAATGCATAGTTTAGTACTAAATGTTACCAACATTTATGTTTACGCTGGTTACGTAGGTTCCTTTAAGTGTGCGAGTGGTTTAAAGACTACCAGCCTATTGCACCTGGGAAACAGGAGGTTGAACATGCATATGAGTGAGTGCACTACTCGCCCTCTCAGATGAACATGGGCATTTGGCCATTTGTAATGTTGCTGCATGGTGCACTTATATGCCTTGATAAGTTTTTCCATTCTAATGTTATATAGTATCAAACGTTCATCATTACTGTGGCTTATGGTCTGGAGTGACGTTTTACAGGTTTGTCAAGAAGAAGTTTGAAGAGCTCTACTTCCAGAGCAGCAAGCCTGACCGTGTGGACCGCGTCTTCAAAATCTACAGAACTACGGCCCTAGACCAGAAACTTGTAAAGAAGACATTCAAGTTGATTGATGAGAGCATGAGACGCTCCAGGGAAGGAACTTGAOther than the expected 2 bp deletion at 3245 and 3246, the substitutionat 1099 (located in the middle of an intron) is the only polymorphismfound between the MSU and our d1 sequences.

What is claimed is:
 1. A genetically modified plant with improved seedproduction in drought conditions and/or improved survival at highplanting densities compared to the seed production of a correspondingplant with no such modification; said modified plant having reducedG-protein activity when compared to a non-modified plant in the sameconditions, said G-protein selected from the group consisting of: Gα,Gβ, Gγ, GPCR, and GCR1.
 2. The modified plant of claim 1 wherein saidG-protein protein activity is created by introducing an inhibitionconstruct to said plant or an ancestor thereof.
 3. Seed of the plant ofclaim
 1. 4. The plant of claim 1 wherein said plant is a maize, cotton,soybean, wheat, barley, rice, rye, oat or sorghum plant.
 5. The plant ofclaim 1 wherein said plant is a rice plant.
 6. The plant of claim 1wherein said G-protein is a G-protein alpha subunit.
 7. The plant ofclaim 1 wherein said modification is a loss of function modification. 8.The plant of claim 1 wherein said plant includes a heterologousconstruct that inhibits expression of a G-protein alpha subunit.
 9. Theplant of claim 1 wherein said plant includes a G-protein alpha subunitexpression cassette that is an inhibitory cassette.
 10. The plant ofclaim 1 wherein said G-protein alpha subunit sequence is SEQ ID NO: 1 or5.
 11. An isolated nucleic acid molecule comprising a nucleotidesequence selected from the group consisting of: (a) the nucleotidesequence set forth in SEQ ID NO:1, or SEQ ID NO:3; (b) a nucleotidesequence which encodes the amino acid sequence of SEQ ID NO:2 or 4; (c)a nucleotide sequence which includes about 90% identity to the fulllength sequence of SEQ I NO:1 or
 3. 12. A nucleic acid constructcomprising a nucleic acid molecule of claim 11, wherein the nucleic acidis operably linked to a promoter that drives transcription in a plantcell.
 13. A plant comprising in its genome at least one nucleic acidmolecule of claim.
 14. Seed of the plant of claim
 13. 15. The nucleicacid construct of claim 12 wherein said construct is an inhibitionconstruct.
 16. A method for conferring or improving seed productionunder drought conditions and/or improved in a rice plant, said methodcomprising: (a) transforming said plant with a nucleic acid moleculecomprising an inhibition construct with a heterologous sequence operablylinked to a promoter that induces transcription of said heterologoussequence in a plant cell; and (b) regenerating stably transformedplants, wherein said heterologous sequence comprises an inhibitionnucleic acid molecule that reduces the activity or expression of one ormore G-protein encoding sequences.
 17. The method of claim 16 furthercomprising obtaining genetically modified progeny plants of one or moregenerations with increased growth in drought conditions.
 18. The methodof claim 16 wherein the inhibition construct is by co-suppression,antisense suppression, or RNAi-mediated suppression.
 19. The method ofclaim 16 wherein the decrease is obtained by introduction of aninhibitory sequence.
 20. The method of claim 17 wherein the progenyplants are obtained by selfing, crossing with another plant or clonalpropagation.